RasMol 2.7.0 March 1999
RasMol 2.7.1 June 1999 RasMol 2.7.1.1 January 2001
RasMol 2.7.2 August 2000
RasMol 2.7.2.1 April 2001
RasMol 2.7.2.1.1 January 2004
RasMol 2.7.3 February 2005
RasMol 2.7.3.1 Apr 06
RasMol 2.7.4 Nov 07
RasMol 2.7.4.1 Jan 08
RasMol 2.7.4.2 Mar 08
RasMol 2.7.5 Jun 09
RasMol 2.7.5.1 Jul 09
RasMol 2.7.5.2 May 11
This version is based directly on
RasMol 2.7.5.1,
RasMol 2.7.4.2, RasMol 2.7.4.1, RasMol 2.7.4,
RasMol 2.7.3.1, RasMol 2.7.3, RasMol 2.7.2.1.1 and on RasMol 2.7.2,
on RasMol 2.7.1.1, on RasTop 1.3,
on RasMol version 2.6_CIF.2, on RasMol version
2.6x1, on RasMol version 2.6.4, and RasMol 2.5-ucb and 2.6-ucb.
Please read the file NOTICE for
important notices which apply to this package and for
license terms (GPL or RASLIC).
This version of RasMol is not in the public domain, but it is given
freely to the community in the hopes of advancing science. If you make
changes, please make them in a responsible manner, and please offer
us the opportunity to include those changes in future versions of RasMol.
Changes from RasMol 2.7.5.1 to RasMol 2.7.5.2 include:
Faster surface rendering by use of NearTree 3.1
Updates to GTK version from T. Ikonen
Use of CBFlib 0.9.2
Use of CQRlib 1.1.2
Minor bug fixes
Changes to RasMol 2.7.5.1 to create RasMol 2.7.5.2:
[24/04/2011] HJB command.c, command.h, molecule.c, molecule.h
Add time command, remove redundant tree builds.
Change flags to NearTree 3.1 interface
[13/12/2009] TPI render.c
PickAtoms(): Use WriteMsg() for text output
DescribeAtom(), PickAtoms(): Reindent
[13/12/2009] TPI gtkwin.c
UpdateScrollBars(): Do not set ReDrawFlag.
Fix screen update on picking labels etc.
Remove unused variables, reindent.
[02/09/2009] HJB maps.c
Change maps to 4.5 sigma cutoff.
[02/09/2009] HJB cmndline.c, command.c
Correct failure to do world rotation in new mouse mode
[09/08/2009] HJB cmndline.c, command.c
Restore general mouse control of bond rotation lost in
2.7.4.2 to 2.7.5 transition
[23/07/2009] HJB maps.c
As per Marian Szebenyi correct the skip of symmetry
ops in CCP4 maps by missing factor of 80.
Changes from RasMol 2.7.4.2 to RasMol 2.7.5 include:
Support for SBEVSL movie commands.
Support for Lee-Richards surface approximation by contouring pseudo-Gaussian electron
densities.
Selection of atoms by proximity to map contours
Coloring of maps by the colors of neighboring atoms
Signficant improvements to the GTK version by Teemu Ikonen
Changes to RasMol 2.7.4.2 to create RasMol 2.7.5.1:
[18/07/2009] HJB .symlinks
Update .symlinks to 2.7.5
[17/07/2009] HJB cif.c command.c raswin_install.nsi
Windows port changes: Update NSIS installer script
Change from mktemp to tmpfile and use rewind not freopen
[17/07/2009] HJB rasmol.doc rasmol.hlp rasmol.html cif.c command.c
rasmol.man rasmol.tex rasmol.vms raswin.rtf
Update doc for 2.7.5, and fix some spacing
[17/07/2009] HJB cif.c x11win.c
Correct X11 file menu for more than 5 open files
Correct cif_read_file CBFlib version to use a temporary file
[16/07/2009] HJB rasmol_install.sh
Correct reporting of font installs for Chinese.X and Japanese.X
[14/07/2009] HJB transfor.c
Fix missing scaling in new translate logic
[12/07/2009] HJB command.c command.h tokens.c trnasfor.c transfor.h
Preliminary movie play logic.
[11/07/2009] HJB command.c
Switch record templates to SSSSSS as per manual
Fix a bug in defer symbol linking
Report undefined symbols in calls to show defer symbol
[10/07/2009] HJB Imakefile_base command.c
Correct Imakefile_base
Add defer/execute movie interaction
[09/07/2009] HJB Imakefile_base rasmol_build_options.sh
Provide new script, rasmol_build_options.sh to reconstruct
new Imakefile from stable Imakefile_base
[09/07/2009] HJB Imakefile rasmol.c
Default Imakefile to use local copies of CQRLIB, CVECTOR,
XFORMSLIB and CBFLIB.
Change from use of fl_init to fl_initialize for xforms-1.0.91
[08/07/2009] HJB Imakefile abstree.c applemac.c cif.stx.tab.c cmndline.c
command.c command.h graphics.h gtkwin.c multiple.c
outfile.c rasmac.c rasmol.c rastxt.c raswin.c render.c
repres.c transfor.c transfor.h wbrotate.c wbrotate.h x11win.c
Partial changes for defer/execute command.
Update versions of external files used in Makefile.
Cleanup of varibables names for saving dial values.
[04/07/2009] HJB command.c maps.c molecule.c pixutils.c rasmol.h repres.c
transfor.c
Clean up errors in map color atom command and remove use
of polys with differing vertex colors by breaking up the
triangles into monchrome subtriangles
[02/07/2009] TPI molecule.c
Add #define _GNU_SOURCE to get the correct definition of basename()
[29/06/2009] HJB command.c
Fix to map select atom add
Add esd to map show for distances to surfaces
and make code for distances to reentrant surfaces more accurate
[25/06/2009] HJB Imakefile command.c molecule.c molecule.h
Update to use of NearTree 2.1.2
Add code to report surface fit stats in map show
[18/06/2009] HJB Imakefile build_MACOSX.sh build_all.sh command.c
rasmol_install.sh tokens.c tokens.h
Add 'add' and 'within' parameters to map select atoms command
Also allow search radius to be specified
[16/06/2009] HJB Imakefile
Update Imakefile for use of installed packages
[14/06/2009] HJB Imakefile
Set up loads of necessary external packages from sourceforge
[13/06/2009] HJB Imakefile applemac.c cmndline.c cmndline.h command.c
graphics.h maps.h molecule.c molecule.h mswin31.c
multiple.c rasmac.c tokens.c tokens.h transfor.c transfor.h
x11win.c
Integrate surface and movie code with gtk code
[03/06/2009] TPI rasmol.c
DisplayUsage(): Revert back to fputs
[27/05/2009] TPI render.c
Do not assume sizeof(Pixel) == sizeof(Long)
Use variables of type Pixel consistently in buffer clearing functions.
Remove version of ClearBuffers() which does not require memset().
[17/07/2009] TPI graphics.h
add startup representation flags
[17/07/2009] HJB rasmol.doc rasmol.html rasmol.man,
Update manual to 2.7.5
[12/05/2009] TPI gtkwin.c
Fix vte input problems by using vte input callback instead of
g_io_watch.
Various file open fixes to GTK version
Fix setting of initial window size.
Fix file open in GTK version: Copy the file name to global var
DataFileName before calling FetchFile.
Add file type filtering to GTK filechooser.
Whitespace fixes.
[12/05/2009] TPI rasmol.c
Fix text output with VTE in GTK interface.
[12/05/2009] TPI command.c command.h rasmol.c
Refactor file opening code. Add support for opening more
than one file from the command line.
Simplify file opening code, remove globs and allow to open files
with spaces and other 'special' characters.
Fix reading files from stdin with '-' arg.
[07/02/2009] HJB command.c command.h rasmac.c rasmol.c rastxt.c raswin.c
tokens.c tokens.h transfor.c transfor.h
Updates to enable the record mode to files. Use with caution,
there are some problems with picking up ReDrawFlag on changes
in appearance. Mouse motion helps to get past the glitch.
[06/02/2009] HJB command.c command.h graphics.h gtkwinc. maps.c rasmac.c
rasmol.c rastxt.c raswin.c tokens.c tokens.h transfor.c
transfor.h
First pass at SBEVSL movie-making commands
[16/11/2008] HJB command.c maps.c
Update to Lee-Richards approximation for probe of given
probe radius with new logic for map spread 0; map scale off;
so that set radius ; map resolution .67; map spread 0;
map scale off; map generate surface produces a good surface
approximation
[20/05/2009] TPI molecule.c
ReviseTitle(): If no identcode, use filename in the title
[20/05/2009] TPI gtkwin.c multiple.c
Update GTK molecule list when a molecule is picked
gtkwin.c: set_gtk_open_file(); new function.
UpdateGtkMoleculeList(); free allocated lists, reindent
multiple.c: SelectMolecule(); call set_gtk_open_file()
[20/05/2009] TPI gtkwin.c rasmol.c
Fix recent files support in GTK version
build_gtkmenu(): Set recent user sort type to most recently used.
Display 30 recent files.
Reindent.
[20/05/2009] TPI printing-resolution.glade sizechooser.glade
Remove useless response_id properties from glade files
[18/05/2009] TPI gtkwin.c rasmol.c
Really fix VTE output in GTK version.
Stop using PTYs for terminal io with VTE.
Don't touch the controlling terminal during init and reset.
Make Delete key work and ignore unhandled terminal escape sequences.
Use custom versions of RasMolExit and RasMolFatalExit in GTK version.
Add some keyboard shortcuts to the GTK GUI.
[18/05/2009] TPI gtkwin.c
Change image export shortcut to C-X
[14/05/2009] TPI rasmol_48x48.xpm Imakefile gtkwin.c
Add an xpm icon for Rasmol.
Set window icon in the GTK version.
[13/05/2009] TPI command.c
revert the filename globbing and extension handling code
[15/02/2009] HJB rasmac.c rasmol.c raswin.c
Clean up handling of ReDrawFlag for appearance changes
[31/10/2008] HJB command.c maps.c
First pass a Lee-Richards surface approximation for map
generate with map resolution 1; map cale off; map level .5;
map generate mesh
Changes from RasMol 2.7.4.1 to RasMol 2.7.4.2 include:
Alignment of command line sizing and positioning options for
Windows and X-Windows version. The command line options -height nnnn,
-width nnnn, -xpos nnnn and -ypos nnnn may be used to set the size
and position of the initial window.
Change of the encoding for Japanese messages and menus from SJIS to
EUC-JP, and corrections to the fontset handling for Chinese and Japanese.
Thanks to Mamoru Yamanishi for contributing the improved fontset logic.
Updates to the rasmol_install.sh and rasmol_run.sh scripts to
support Chinese and Japanese using cxterm.
Optional use of GTK. Thanks to Teemu Ikonen for the new GTK code.
Changes to RasMol 2.7.4 to create RasMol 2.7.4.1:
[18/03/2008] HJB graphics.h mswin31.c rasmol.c rastxt.c
raswin.c x11win.c
Add global InitWidth, InitHeight, InitXPos, InitYPos
to support common implementation of command line
options -height nnnn -width nnnn -xpos nnnn -ypos nnnn
to control initial window size and position
[18/03/2008] HJB x11win.c
Redo Japanese and Chinese fontset logic as per suggestion
by Mamoru Yamanishi
[18/03/2008] HJB Imakefile
Allow use of old X locale.
[18/03/2008] HJB langsel_unix.c
Switch Japanese for unix from SJIS to EUC-JP, introducing
langsel_unix.c
[21/02/2008] TPI actionmenu.gtk egg-macros.h eggfileformatchooser.c
eggfileformatchosser.h graphics.h gtkwin.c Imakefile
multiple.c printing-resolution.glade rasmol.c sizechooser.glade
transfor.c wbrotate.c
Addition of GTK interface by T. Ikonen, including new routines
actionmenu.gtk egg-macros.h eggfileformatchooser.c
eggfileformatchosser.h gtkwin.c printing-resolution.glade
sizechooser.glade
Changes from RasMol 2.7.3 to RasMol 2.7.4.1 include:
Support for maps.
Message and menu translations for Russian, Bulgarian, Japanese and Chinese.
Our thanks to G. Pozhvanov, G. Todorov, Nan Jia, Mamoru Yamanishi and Katajima Hajime.
Fix torsion angle calculation as per bug report and patch by Swati Jain.
Corrections by Ladislav Michnovic to port to more platforms.
Code to read remediated PDB entries as suggested by Huanwang Yang
Updated icons.
Extended export menus.
Changes to RasMol 2.7.4 to create RasMol 2.7.4.1:
[19/01/2008] HJB
Release 2.7.4.1 created
[18/01/2008] HJB command.c, maps.c, maps.h, molecule.c
mswin31.c outfile.c outfile.h pixutils.c pixutils.h
rasmac.c, repres.c
Add LoadCCP4MapFile. Extend range of stereo angle to
60 degrees. Add GM notoggle command. Add code to
avoid trying to reuse a zapped map. Increase default
map resolution to 1 Angstrom. Change mapdata to
void * and use memmove to allow multiple data types,
add fields for number of grid divisions, map type,
element size and element type. Add code to load
and save maps in CBFlib format. Fix stereo.
[16/01/2008] HJB vector.c wbrotate.c
Fix multiple definitions of PI.
[14/01/2008] LM infile.c
Add include of string.h as per Ladislav Michnovic.
[14/12/2008] HJB graphics.h
Add buffers for slab and depth pixel-by-pixel
cutoff values.
[10/12/2007] GM langsel.c langsel.h languages/README.txt
languages/genlanselall languages/langsel*.utf.c,
tokens.c tokens.c
Corrected japanese langsel encoding. It is now
Shift_JIS.Added messages for NoToggle and ColourMode
commands. Updated langsel README.txt. Add NoToggle
and ColourMode commands
[06/12/2008] GM command.h
Add NoToggle and ColourMode variables.
[25/11/2007] HJB cif_fract.c
Rewrite calculation of matrix inverse.
Changes to RasMol 2.7.3.1 to create RasMol 2.7.4:
[19/11/2007] HJB
Release 2.7.4 created
[19/11/2007] HJB abstree.c abstree.h
Break out element identification from GetElemNumber
into GetElemDescrNumber. Fix torsion angle calculation
as per bug report and patch by Swati Jain.
[19/11/2007] HJB applemac.c
Add code to make languages sticky. Add register and
donate menu items, make languages sticky and launch
browsers.
[19/11/2007] HJB cif_fract.c
Correct calculation of matrix transforming orthogonal
to fractional coordinates and rewrite matrix
transforming fractional to orthogonal.
[19/11/2007] HJB command.c command.h
Add code for map commands. Make CommandError accessible
from other routines. Add Raster3D write/save option.
Allow proberadius of 6 Angstroms. Add Bulgarian,
Chinese, Japanese and Russian commands. Allow
spacefill up to 12 Angstroms. Allow mirror and
rotate suboptions on write/save.
[19/11/2007] HJB font.h, graphics.h
Allow access to font parameters and support info
[19/11/2007] HJB Imakefile
Add use of CBFlib
[19/11/2007] HJB infile.c
Make sensitive to PDB version to allow for handling of
remediated files, based on changes suggested by
Huanwang Yang of the RCSB PDB in April 2007.
[19/11/2007] GT langsel.c languages/
langsel.c restructured to be generated from separate
language files in the directory languages/
[19/11/2007] HJB molecule.c molecule.h
Add atom type processing and DA, DC, DG, DT, DI for
remediated PDB DNAs, based on changes suggested by
Huanwang Yang of the RCSB PDB in April 2007.
[19/11/2007] HJB multiple.c multiple.h
Manage map data for multiple molecules. Increase the number
of molecules from 5 to 15. Increase the number of characters
in the name to 33 characters.
[03/12/2006] HJB outfile.c
Clean up compilation warnings in outfile.c
[19/11/2007] HJB outfile.c outfile.h
Add Raster3D support based on code by V. Stanev. Partial
Vector PS map support.
[19/11/2007] HJB pixutils.h
Fix stereo of ribbons and map surfaces. Protect against
duplicate definition of Knot struct. Make ClipPolygon
accessible.
[19/11/2007] HJB rasmac.c rasmac.h
Increase terminal window to 132 characters. Add About dialog.
Clean up maps on exit. Add support for Russian, Bulgarian,
Chinese and Japonese. Add register and donate browser calls.
Add G4 CPU type. Extend export file types.
[19/11/2007] HJB RasMac.r
Update icons to new style. Extend Export menu to BMP...,
GIF..., IRIS RGB..., PPM..., Sun Raster, PostScript, PICT...,
Vector PS ..., Molscript ..., Kinemage ..., POVRay 3 ...,
VRML ..., Ramachandran ..., Raster3D ..., RasMol Script ....
Extend Apple menu to About RasMol..., RasMol Help ...,
Register ..., Donate ....
[19/11/2007] HJB rasmol.c
Update to release 2.7.4 with map support.
[19/11/2007] HJB script.c script.h
Add code to write out scripts for maps.
[19/11/2007] HJB string_case.c string_case.h
Fix case sensistive of last character comparison of strcasecmp and
strncasecmp. Add str255casecmp, strcasestr.
[19/11/2007] HJB tokens.c tokens.h
Add tokens for Average (MeanTok), Bulgarian (BulgarianTok),
Chinese (ChineseTok), Contour (ContourTok = LevelTok),
Generate (GenerateTok), Japanese (JapaneseTok), Level (LevelTok
= ContourTok), Map (MapTok), Mask (MaskTok), Mesh (WireframeTok),
Mirror (MirrorTok), New (NewTok), Next (NextTok), R3D or
Raster3D (Raster3DTok), Resolution (ResolutionTok), Spacing
(SpacingTok), Spread (SpreadTok), Width (SpreadTok),
[19/11/2007] HJB transfor.c transfor.h
Add map point colouring routines, ColourPointAttrib and
ColourPointPotential.
[19/11/2007] HJB x11win.c
Extend Export menu to BMP ..., GIF ..., IRIS RGB ..., PPM ...,
Sun Raster, PostScript, PICT ..., Vector PS ..., Molscript ...,
Kinemage ..., POVRay 3 ..., VRML ..., Ramachandran ...,
Raster3D ..., RasMol Script .... Enable and extend Help
menu to About RasMol..., User Manual..., Register...,
Donate.... Set locale for each langauge and use fontsets.
Use table of languages versus fonts in langsel. Add
About splash screen and revise popup logic to handle it.
Change text metrics to allow for Chineses and Japanese.
Try to make lack of access to shared memory non-fatal.
[03/10/2007] PK molecule.c
"RasMol - " string added to the title of the window.
[03/10/2007] PK multiple.c
Window title is updated when different molecule is selected.
[02/02/2007] HJB rasmol.c
Remove // comments for AIX build. Fix signed length conflict
[01/03/2007] GT rasmol.c
Chinese version.
[23/12/2006] HJB x11win.c
Detect remote X server that does not share memory
[29/12/2006] HJB rasmol.c x11win.c
Update x11win.c and rasmol.c to add links to list of browsers
and to kill About dialog when the menu bar is selected
[29/12/2006] HJB rasmol_install.sh
Update rasmol_install.sh to allow recompilation of fonts
on install to handle openwin and other old systems that
can't handle byte-swapped bdf files, and add enviroment
variable RASMOL_NOSPAWN to suppress spawn in intermediate
xterm from rasmol_run.sh. -- HJB
[23/12/2006] HJB rasmol_install.sh, rasmol_run.sh scripts
Add new rasmol_install.sh and rasmol_run.sh scripts
[29/11/2006] HJB raswin.idm
Fix missing raswin.idm in src.
[29/11/2006] HJB rasmol.c
Add missing include of sys/stat.h in rasmol.c
[10/12/2006] HJB x11win.c
Additional updates for linux build with Russian, cleaning
up X11 font selection for CP1251 and recovering when fonts
are missing. -- HJB
[03/12/2006] HJB x11win.c
Mods for about screen under Linux -- HJB
[28/11/2006] HJB x11win.c
Changes for Russian and About dialog in unix
[20/10/2006] HJB wbrotate.c
Localize " not found!" message in RemoveBond and CreateBondAxis
[16/09/2006] HJB x11win.c rasmol.c
Start of RasMol Russian Translation Project based on translations
by Gregory A. Pozhvanov of Saint Petersburg State University.
[11/02/2006] HJB script.c script.h
Add mirror and rotate options for VRML.
Changes from RasMol 2.7.2.1.1 (the final reference release
of RasMol 2.7.2) to RasMol 2.7.3.1 include:
Adjustment to the mouse handling for a better, more natural feel. Our thanks
to C. Chigbo for the suggestion.
Correction to cif.c for blanks after an initial quote mark.
Correction to mswin31.c to restore lost initializations of ZRange
and DialValue[8..9].
Modifications by Mamoru Yamanishi to Imakefile and rasmol.c
to use xforms
for GUI file open.
This patch needs the opens source xforms 1.0.90 library by
Steve Lamont.
Correction to molecule.c to correct input of xyz files. Thanks
to Stuart Prescott.
Revision to CPK colors by C. Chigbo.
The new colors are called CPKNEW. The current CPK colors remain available
as CPK.
Correction to negative torsion angle monitors and to
imprecise distance and angle monitors by C. Chigbo.
This patch corrects the display of negative torsion angles caused by use of
the unsigned short type, and correctys imprecise distance and angle displays.
This extends the original patch which was just for torsion angles (torsion.patch).
A side effect of this change is to limit the available range for distance monitors
to approximately 327 Ångstroms.
Initial code for display of solid Lee-Richards molecular surfaces.
This patch adds the basic code for display of Lee-Richards surfaces with a
new Molecular Surface menu item, and surface molecule <probe radius> and
surface solvent <probe radius> commands.
Corrections of ribbons 0, etc. commands by R. Chachra.
With this patch, the wireframe 0, ribbon 0, cartoon 0,
backbone 0, strands 0 and trace 0 commands work the same as these
command with off instead of 0.
Changes to RasMol 2.7.3 to create RasMol 2.7.3.1:
[21/04/2006] HJB rasmol.h RasMac.r raswin.rc
Update version to 2.7.3.1
[21/04/2006] CC abstree.c render.c repres.c repres.h
Fix by Clarice Chigbo to improve accuracy of
distance calculations by changing from Long to
double. Report model number. Use Long instead
of short for monitors.
[15/12/2005] HJB x11win.c
Fix mouse runaway by removing conflict of HeldStep
and HeldButton variable name use.
[16/07/2005] HJB abstree.c infile.c render.c
Correct sign errors in use of ztrl
Changes to RasMol 2.7.2.1.1 to create RasMol 2.7.3:
[06/02/2005] HJB
Release 2.7.3 created
[21/01/2005] HJB molecule.c
Correct XYZ input by capping atom types. Thanks to
Stuart Prescott.
[16/01/2005] HJB applemac.c, cmndline.c, command.c, command.h,
infile.c, langsel.c, langsel.h, langsel_mac.c,
molecule.c, molecule.h, mswin31.c, multiple.c,
pixutils.c, pixutils.h, rasmac.c, rasmol.c,
rastxt.c, raswin.c, render.c, render.h, repres.c,
repres.h, tokens.c, tokens.h, transfor.h, x11win.c
Base level of changes for Lee-Richards molecular
surfaces.
[12/01/2005] Clarice Chigbo repres.c, render.c, repres.h
Correction to negative torsion angle monitors and to imprecise
distance and angle monitors; limits the available range for
distance monitors to approximately 327 Angstroms.
[17/01/2005] Clarice Chigbo script.c
Output CPKNEW in scripts
[04/01/2005] Ricky Chachra command.c
Fix to wireframe 0, ribbon 0, cartoon 0, backbone 0,
strands 0 and trace 0 commands to work the same as these
command with off instead of 0
[30/10/2004] Mamoru Yamanishi Imakefile, rasmol.c
Used xforms to provide GUI for file open under X-windows
[21/10/2004] Clarice Chigbo tokens.c, tokens.h
Define CPKNEW token
[20/10/2004] Clarice Chigbo transfor.c, transfor.h
New CPK color table
[26/04/2004] HJB cif.c
correction to handling of blank immediately following
initial quote mark.
[26/04/2004] HJB vector.c
correction to SubtractAtoms for bond rotation.
Changes from RasMol 2.7.1 (the final reference release
of RasMol 2.7.2) to RasMol 2.7.2.1.1 include:
Post release patches to command.c were included to fix the
handling of load inline in the UCB multiple molecule environment. In
addition conditional code controlled by STRICT was disabled to restore
operation of load inline under windows. Thanks to Jan Reichert
<jr@imb-jena.de> for pointing out these problems. Thanks to E. Martz
<emartz@microbio.umass.edu> for pointing out an error in the Spanish
translation credits which has been corrected.
Thanks to a report by Julien Hering, the omission of a prior fix to the MS Windows
version was found and corrected on 7 May 2004.
Adaption of the multilingual mods from RasMol 2.7.1.1 into Rasmol 2.7.2.1.
Rewrite of the mouse handling and rotation logic to correct the
problems in 2.7.2 and make the feel of 2.7.2.1
closer to that of RasMol 2.7.1.
Addition of French menus and messages
Addition of Italian menus and messages
Adoption of picking for selection of atoms, groups or chains from
RasTop 1.3.
Adoption of backclipping from RasTop 1.3
Adoption of shadepower command for glassy surfaces from RasTop 1.3
Change of the menu stereo option to rotate cross-wall-none
Allow longer atom names (12 characters) in CIFs.
Incorporation of some of the code from the UCB RasMol variants.
Out thanks to Eileen Lewis and Marco Molinaro for their cooperation
in contributing the UCB Enhanced RasMol code for incorporation
into the RasMol 2.7 series.
Code to represent bonds in and to alternate conformers with
a narrowed portion in the middle of each bond.
An attempt to fix some of the chirality reversals in some of the
output modes.
Fixes for some of the problems reported since the last release.
Post-release changes to RasMol 2.7.2.1.1:
[07/05/04] HJB mswin31.c
restored lost fix for intialization of ZRange and
DialValue[8..9] and rebuilt raswin.exe. Thanks to
Julien Hering.
[14/02/04] HJB pixutils.c
remove static from declaration of ClipVector.
[14/02/14] HJB cif_stx.c
remove trailing characters from #endif.
[03/02/04] HJB Makefile.in
Change transfer to transfor in 2 dependencies. Thanks
to R. Harlow.
Changes to RasMol 2.7.2.1 to create RasMol 2.7.2.1.1:
[26/01/04] HJB abstree.c
Fix warning on sprintf calls with unused args, match long
variables with %ld format descriptors.
[26/01/04] HJB cif.c
Add brackets to avoid compiler warnings on dangling elses.
Fix cif_lex to parse 'O''' correctly. Change from
WORD to CIFWORD to avoid conflict with windows.h.
[26/01/04] HJB cif.h
Change from WORD to CIFWORD to avoid conflict with windows.h.
Add prototype for cif_free_handle.
[26/01/04] HJB cif.stx.tab.c
Change from WORD to CIFWORD to avoid conflict with windows.h.
[26/01/04] HJB cif_ctonum.c
Remove unused variable dndec
[26/01/04] HJB cif_fract.c
Remove unused variable kk
[26/01/04] HJB cif_stx.c
Change from WORD to CIFWORD to avoid conflict with windows.h.
Add include of rasmol.h.
[26/01/04] HJB command.c
Initialize variables to avoid compiler warnings. Use %ld
format for long variables. Fix RotMode == RotBond which
should have been an assignment. Add parens on logical
expressions.
[26/01/04] HJB command.h
Add prototypes for ResumePauseCommand, InterruptPauseCommand.
[26/01/04] HJB graphics.h
Add include of windows.h
[26/01/04] HJB infile.c
Removed unused ReadValue2. Add brackets to avoid compiler
warnings on dangling elses. Initialize variables to avoid
compiler warnings.
[26/01/04] HJB langsel.c langsel_mac.c
Add include of string.h
[26/01/04] HJB molecule.c
Add include of graphics.h. Change to %ld format for longs.
Remove unused variables. Add brackets to avoid compiler warnings
on dangling elses.
[26/01/04] HJB molecule.h
Add prototype of TestDisulphideBridge.
[26/01/04] HJB multiple.c
Fix reversed comment terminator. Add include of string.h. Add
brackets to initializer to match structure.
[26/01/04] HJB multiple.h
Add prototype of ReRadius.
[26/01/04] HJB outfile.c
Initialize variables to avoid compiler warnings. Change to %ld
for long.
[26/01/04] HJB pixutils.c
Initialize variables to avoid compiler warnings. Removed unused
variables.
[26/01/04] HJB pixutils.h
Add prototypes of DrawTwinLine, ClipLine, ClipTwinLine,
ClipDashLine, DrawTwinVector, ClipVector, ClipTwinVector,
ClipDashVector.
[26/01/04] HJB rasmol.c
Add parens to avoid compiler warning.
[26/01/04] HJB rasmol.h
Set version and date. Add include of stdlib.h for malloc.
[26/01/04] HJB render.c
Change the handling of very long longs to avoid a compiler
warning. Use %ld format for longs.
[26/01/04] HJB repres.c
Remove unused variables. Use %ld format for longs. Initialize
variables to avoid compiler warnings.
[26/01/04] HJB repres.h
Add prototype of LoadDotsFile.
[26/01/04] HJB script.c
Add include of string.h. Use %ld format for longs. Initialize
variables to avoid compiler warnings. Remove unused variables.
Fix sign of trailing bits on VRML z coordinates.
[26/01/04] HJB script.h
Add prototype of WritePOVRay3File.
[26/01/04] HJB tokens.h
Add parens in definition of IsImageToken.
[26/01/04] HJB transfor.c
Add parens for logical expression. Remove unused variables.
Initialize variables to avoid compiler warnings.
[26/01/04] HJB transfor.h
Add prototype of DefineShade, RMat2RV, RV2RMat.
[26/01/04] HJB wbrotate.c
Add include of cmndline.h. Remove unused variables. Initialize
variables to avoid compiler warnings. Use %ld format for longs.
Add value for a returns that need them.
[26/01/04] HJB x11win.c
Initialize variables to avoid compiler warnings. Add brackets to
avoid compiler warnings on dangling elses.
[14/04/02] HJB Imakefile
Update to allow scripts to make multiple pixel depths by
setting PIXELDEPTH to 8, 16 or 32 externally. Add default
flags for various HP architectures.
[13/04/02] HJB cif.c
Reduce warnings by casting uses of size_t.
[13/04/02] HJB cif_ctonum.c
Reduce warnings by casting to int for pointers indptr-test.
[13/04/02] HJB command.c
Reduce warnings by explicit use of long (rather than Long)
for fpos, and casting to size_t for comparisons, etc.
[13/04/02] HJB infile.c
In ProcessPDBBond, match types of srcatm and dstatom by
changing from int to Long, casting to size_t for
comparisons, etc.
[13/04/02] HJB molecule.c
Change MemSize from int to size_t.
[13/04/02] HJB rasmol.c
Change AdviseLen from int to size_t, change socket to xsocket,
change __hpux to HPUX_LEGACY
[13/04/02] HJB rasmol.h
Add HPUX_LEGACY for old style hpux select.
[13/04/02] HJB render.c
Make test of sizeof(Long) > 4 conditional on not defining
_LONGLONG. Make some changes from Long to long, etc.
[13/04/02] HJB x11win.c
Cast some pointer diffs to int, change some Long to long,
etc.
[29/06/01] HJB command.c
Correct logic for inline load of a new molecule from
data file treated as a script.
[21/04/01] HJB all
Fix credit for initial Spanish translation. Thanks to
E. Martz.
[19/04/01] HJB command.c
Post release fix to handling of load inline in
windows version due to problem with STRICT logic.
Thanks to Jan Reichert for pointing
out the problem.
[18/04/01] HJB command.c
Post release fix to handling of load inline in UCB
multiple molecule environment. Thanks to Jan
Reichert for pointing out the
problem.
Changes from RasMol 2.7.1.1 and 2.7.2 to create RasMol 2.7.2.1:
[14/04/01] HJB script.c
Correct error in writing scripts with partial use of spacefill.
Thanks to Steven Vik for reporting the
problem.
[14/04/01] HJB rasmol.doc, itasmol2721.hlp, esrasmol.html
Updated manuals for 2.7.2.1.
[02/04/01] HJB abstree.c, abstree.h
Increase space for atom names from 4 to 12 characters.
[02/04/01] HJB applemac.c
Add symbolic ZRange, add 2 dials. See [12/01/01] changes for langsel.
[02/04/01] HJB cmndline.c, cmndline.h
Reworked all exits on mouse motion processing to leave values
in DialValues or WRot..., etc depending on RotMode. Made HeldButton
a global for future reference.
[02/04/01] HJB command.c, rasmol.c, rasmac.c, raswin.c
Change stereo command to cycle cross-wall-none.
[02/04/01] HJB command.c, script.c, transfor.c
Rework output of rotation information.
[02/04/01] HJB infile.c
Increase limit on atom names for CIF from 4 to 12 characters.
[02/04/01] HJB langsel.c langsel_mac.c
Add French (thanks to Jean-Pierre Demailly
) and Italian (Giuseppe Martini
and Giovanni Paolella
with contributions by: A. Davassi, M. Masullo, C. Liotto, G. Paolella,
G. Martini. Adapt to 2.7.2 menu structure.
[02/04/01] HJB mswin31.c
Removed "Printing Completed" message.
[02/04/01] HJB multiple.c
Save DotPtr to fix misplaced dots in multiple molecules. Save
LastTX, LastTY, LastTZ, LocalRadius, ShiftS, XlateCen. Make
"Insufficient memory" message be language dependent
MsgStrs[StrMalloc]
[02/04/01] HJB outfile.c, pixutils.c, repres.c
Rework backclipping separating ZOffset from new DepthValue,
define BitBack
[02/04/01] HJB tokens.c
Added the following tokens relative to 2.7.2, includes tokens
added for 2.7.1.1:
ASSE AxesTok
ASSI AxesTok
CADENA ChainTok
CADENAS ChainTok
CATENA ChainTok
CATENE ChainTok
COPY CopyTok
DEPTH DepthTok
DIBUJO CartoonTok
DIBUJOS CartoonTok
E AndTok
EJE AxesTok
EJES AxesTok
ELANCE BondTok
ELANCES BondTok
ELICHE HelixTok
ENGLISH EnglishTok
ELICHE HelixTok
ESQUELETO BackboneTok
ETIQUETA LabelTok
ETIQUETAS LabelTok
ETICHETTA LabelTok
ETICHETTE LabelTok
FILODIFERRO WireframeTok
FILDIFERRO WireframeTok
FILI StrandsTok
FRENCH FrenchTok
GIRO TurnTok
GIROS TurnTok
GRUPO GroupTok
GRUPPO GroupTok
HEBRAS StrandsTok
IMAGE ImageTok
ITALIAN ItalianTok
MOSTRAR DisplayTok
NASTRO RibbonTok
NASTRI RibbonTok
PASTE PasteTok
POSITION PositionTok
RIEMPIMENTO SpacefillTok
SALIR ExitTok
SCHELETRO BackboneTok
SELECTION SelectionTok
SHADEPOWER ShadePowerTok
SPANISH SpanishTok
TODO AllTok
TUTTO AllTok
VIEW ViewTok
VIGNETTA CartoonTok
VISUALIZZA DisplayTok
[02/04/01] HJB transfor.c
Rework interaction of mouse, local rotation and world rotation
to make horizontal mouse motion of individual molecule rotate
horizontally even when outer world rotation creates a tilt.
Restores incremental mouse motion effects similar to what
was in effect for 2.7.1, but with world rotations. Reworked
RasTop centering to restore 2.7.2 behavior -- defaults to
center the new rotation on the screen.
[02/04/01] HJB several
Make dial indices symbolic.
[02/04/01] HJB wbrotate.c, wbrotate.h
Rework interaction of mouse and world rotation to make
horizontal mouse motion of individual molecule rotate horizontally
even when outer world rotation creates a tilt.
Changes adopted from RasTop 1.3 in creating RasMol 2.7.2.1:
Note: These mods do not reflect the complete source of RasTop 1.3.
[31/01/00] PV command.c
Added code for selecting atom areas with mouse: changed
PickAtom() function name in PickAtoms(); changed PicAtome
identifier in PickAtom; added function SelectArea()
and DisplayArea(); added code for command "select view"
[30/01/00] PV command.c
Added command "select view" and corresponding code,
which allows to select a part of a molecule based on screen display.
[16/01/00] PV cmndline.c
In PerformMouseFunc() corrected MM_CLIP to access clipping with
the mouse, added MM_DEPT to access backclipping (depth) with the mouse.
[16/01/00] PV transfor.h, transfor.c, token.h, token.c, script.c
Added ShadePower in DefineColourMap(), which brings some interesting
shade variations. Added ShadePowerTok and command "set shade x"
with x between -20 to 20.
[03/01/00] PV transfor.c
Fixed bug (and modified) function Power() to handle Specpower
[12/14/99] PV
Added variables ShiftS and UseAutoDepthCue that adjust DepthCue
with slabbing.
[14/12/99] PV transform.c
Added function CentreTransform() to either move the origin in the
molecule or move the molecule to the origin (origin = True ).
Added variables Cenx,y,z, which mesure distance centre-origin.
[29/09/99] PV molecule.c
Fixed bug in FindCisBonds() (no zeroing of last group cisbondflag);
Added ability to convert triple bond to single (CreateBondOrder())
[24/09/99] PV cmndline.c
Correlated mouse binding to global variable MouseMode.
Removed EnableMenus(state==1) in ResetCommandLine().
Fixed mouse binding with INVERT on y values.
Fixed bug on capture status on mouse-up. Added MM_PREV
to mouse binding for deselection. Fixed INVERT on y
value for mouseup.
[21/09/99] PV command.c, render.h, render.c, transfor.h, transfor.c
Added four new picking modes: select an atom: PickAtom; select
a group: PickGroup; select a chain: PickChain; modify bonding/add
multiple bonds: PickBond. Allowed picking parameter shift = -1
when Ctrl key is down to deselect an atom (a group, a chain)
from the current selection. [Note by HJB 02/04/01 -- The UCB
and 2.7.2 bond picking was used in 2.7.2.1 instead of the
RasTop version]
[22/09/99] PV abstree.h, abstree.c
First step for saving atomsets & identifiers in RasMol scripts
(SetSize to 100 and SymEntry and SymbolTable in header).
[21/09/99] PV cif.h
Fixed missing declaration of cif_parse in cif.h
[21/09/99] PV cmndline.c
In ProcessCharacter()) added ESC (0x1b) character to interrupt
script pausing.
[21/09/99] PV command.c
Changed output for one-letter-code sequence in series of 50
characters with a space each subgroup of 10.
[21/09/99] PV infile.c
Compiling problems with RasMol 2.7.1 files (VisualC++ 5.0)
- explicited all conversions long to short in infile.c /*casting*/
[21/09/99] PV pixutils.c
Compiling problems with RasMol 2.7.1 files (VisualC++ 5.0)
- fixed casting in drawstar() and clipstar() in pixutils.c
Set ARCSIZE to 32768 under MSWIN, allowing drawing cylinders with
radii up to 250 RasMol Units. Current implementation gives a maximum
of 75 RU at maximum zooming. Mac implementation should be verified.
[14/07/99] PV abstree.c transfor.c
(Adapted from RasTop 1.3) Added shortcuts for direct evaluations
of atomsets (BuildAtomSet(), SelectZoneExpr()).
[14/07/99] PV abstree.c, transfor.c
Added shortcuts for direct evaluations of atomsets (BuildAtomSet(),
SelectZoneExpr()); gain up to 15 seconds of computer time on very
large molecules.
[10/07/99] PV cif.c
Fixed memory allocation bug in cif_make_handle
Changes from RasMol 2.7.1 to create RasMol 2.7.2:
[28/08/00] HJB all
Updates to comments, resources, etc for preliminary testing
release.
[21/08/00] HJB abstree.c, abstree.h
Change type Atom to RAtom to avoid conflicts with X.
Offset all uses of xorg, yorg, zorg databse entried with
fxorg, fyorg, fzorg database entries for UCB bond
rotation. Change char* strings to unsigned char* strings
to allow for extra UCB Angstrom and degree symbols.
[21/08/00] HJB applemac.c
Change from use of toolbar settings to use of RotMode.
Add new "Settings" menu.
[21/08/00] HJB cmndline.c
Adapt GSG code from UCB mods for mouse moves, to make
the moves control bond rotation, molecule rotation, or
world rotation, but change from use of toolbar settings
to use of RotMode
[21/08/00] HJB command.c
Add new error message (ErrNoBond) for "Bond for rotation
not picked". Add new parameter for alternate conformer
bond waist radius. Adapt to fxorg, etc. offsets. Adapt
GSG UCB pick bond tool bar button to a command line
command. Add show centre, show rotation, show translation
and show zoom commands. Add bond, unbond commands.
Add rotate bond, rotate molecule, rotate all command.
[21/08/00] HJB command.h
Add space after "__huge"
[21/08/00] HJB font.h
Adapt GSG UCB mods characters for Angstrom and degree to be
additional symbols, not repalcements.
[21/08/00] HJB graphics.h
Add new redraw flag, "RFRotBond" to signal that a bond
rotation is involved, and add it to RFRotate, RFApply and
RFInitial. Add ZRange. Move main X window definitions
into this header to facilitate toolbar development.
[21/08/00] HJB infile.c, infile.h
Change all Atom types to RAtom. Add xorg, etc. offsets
on all coordinate calauclations. Move GroupPool definition
to header.
[21/08/00] HJB molecule.h and all referring files
Change type Atom to RAtom to avoid conflicts with X.
Add fxorg, fyorg, fzorg database entries for UCB bond
rotation offsets.
[21/08/00] HJB multiple.c
Remove all use of the toolbar, converting to menu.
Detect last element of file name string. Update VarList
for current variables. Change to ANSI C prototypes.
Move revised DrawMoleculeList from GSG's UCB toolbar.c
into multiple.c, but drop list only into MolName[].
[21/08/00] HJB wbrotate.c, wbrotate.h
Remove all use of the toolbar, converting to menu.
Change to ANSI C prototypes. Revise bond and world
rotation logic to use full rotation, nor increment,
for improved accuracy. Change Bond rotation logic to
preserve nesting of bonds without changing the original
coordinates. Add database of selected bonds and logic
to add bonds on the fly and remove them.
[21/08/00] HJB vector.c, vector.h
Change to ANSI C prototypes. Replace Vector and Matrix
with their array definitions for clarity.
[27/02/00] HJB transfor.c, transfor.h
Add alternate conformer bond radius to EnableWireFrame
[23/02/00] HJB infile.c
Fix *- for - typo in XYZ and MOL2 input of coordinates
[23/02/00] HJB molecule.c
Fix D2O to DOD mapping. Thanks to Brian W. Beck.
[23/02/00] HJB pixutils.c
New code for alternate conformer bonds.
[23/02/00] HJN raswin.c
Update WinMail entry to WINAPI
[29/01/00] HJB molecule.c
Comment out chain by chain reset of bonding to allow for
het groups after TER at expense of slower bonding.
[29/01/00] HJB mswin31.c
Update printer logic for modern windows specs.
[29/01/00] HJB rasmac.c
Fix reference of monaco font.
[15/07/99] HJB (for AR) raswin.c
Add check for \r. Thanks for Andrew Raine.
[15/07/99] RS raswin.c
Add .ML2 and .SY2 extensions for Sybyl and MOL2.
Changes adapted from UCB rasmol in creating RasMol 2.7.2:
Note: These mods do not reflect the complete source of UCB RasMol.
In particular toolbar.h and toolbar.c have not been used in this pass,
and the full source of UCB RasMol has not yet been recovered.
[30/11/95] GSG rasmac.c
Hide command window. Add help screen menu logic. Add hooks to
load multiple molecules. Add toolbar menu to Windows menu. Make
mouse moves control bond rotation, molecule rotation or world
rotation depending on tool bar button choices. Same for scroll
bars.
[29/11/95] GSG applemac.c
Change default background for printing to white.
Hook scroll bar H values to bond angle (BRotValue),
molecule rotation angle (DialValue[1]) or
world rotation angle (WRotValue[1]) depending on
toolbar settings. Hook scroll bar V values to
molecule rotation angle (DialValue[0]) or
world rotation angle (WRotValue[0]) depending on
tool bar settings. Allow file open when less than
MAX_MOLECULES molecules.
[21/08/00] GSG font.h
Add characters for Angstrom and degree as replacements
for vertical bar and tilde.
[16/11/95] GSG render.c, render.h
Add PickBond. Add hooks to draw multiple molecules. Automatically
switch to the molecule of any picked atom. Add monitor for picked
distance, angle or torsion angle.
[14/11/95] GSG transfor.c
Add hooks for bond rotation and global rotation.
[14/11/95] GSG vector.c, vector.h, wbrotate.c, wbrotate.h
New routines introduced with UCB mods to allow for
bond rotations and global rotation.
[14/11/95] GSG infile.c
Add fxorg, fyorg, fxorg for MDL molecule input only.
[14/11/95] GSG molecule.c, molecule.h
Add fxorg, fyorg, fxorg and list of bonds to atom database
for world and bond rotation.
[11/11/95] GSG multiple.c, multiple.h
New routine introduced with UCB mods to allow for
multiple molecules.
[10/11/95] GSG tokens.c,tokens.h
Add MoleculeTok.
[10/11/95] GSG repres.h
Add flag for units to Monitors.
[09/11/95] GSG command.c, command.h
Add hooks for multiple molecules. Log background
status to allow default white print background.
Add molecule command.
[09/11/95] GSG rasmol.c
Add initialisation for multiple molecules.
Changes from RasMol 2.7.1 to create RasMol 2.7.1.1:
[21/01/01] FGR, HJB langsel.c, langsel_mac.c, mswin.c, applemac.c
Installed translations for Edit menu on mac and PC
provided by Fernando Gabriel Ranea.
[17/01/01] FGR, HJB langsel.c, langsel_mac.c
Corrections to translations by Fernando Gabriel Ranea, installed
by HJB with revisions to menu bar accelerators.
[12/01/01] HJB applemac.c
Added include of langsel.h. Added routine ReWriteStr255 to rewrite
menu bar items in place and tostr255 to convert other menu items
strings to Pascal form for use in SetmenuItemText. Set up
ReDrawWindow to refresh all menu strings and then redraw the menu
bar. Note that the rewrite of the main menu bar is _very_ risky
and may not survive system changes.
[12/01/01] HJB command.c
Added include of langsel.h. Remove redundant ErrorMsg array and Err...
definitions. Change messages to reference MsgStrs. Add English and
Spanish as commands calling SwitchLang.
[12/01/01] HJB infile.c
Fix coordinate typo in load of XYZ and Mol2 molecules.
[12/01/01] HJB langsel.c, langsel_mac.c, langsel.h
New routines to carry multi-lingual translations. Many thanks to
Fernando Gabriel Ranea for the bulk of the Spanish translations,
and for creating the initial Spanish version of RasMol 2.7.1. Note
that langsel.c uses the ANSI character set, while lansel_mac.c uses the
Macintosh character set.
[12/01/01] HJB molecule.c
Added include of langsel.h. Changed messages to reference MsgStrs.
Refixed D2O misparse, which had been previously fixed. Mod had been
lost.
[12/01/01] HJB mswin31.c
Added include of raswin.idm and langsel.h. Included partial update
to printer logic. Added ReDrawWindow as rewrite of menus with
ModifyMenu and RemoveMenu/AppendMenu calls.
[12/01/01] HJB rasmac.c
Added include of langsel.h. Added SwitchLang(English) calls
for initialization to main routine.
[12/01/01] HJB rasmol.c
Add fix for broken math routines by referencing atan2.
[12/01/01] HJB rasmol.h
Added include of langsel.h. Added SwitchLang(English) calls
for initialization to main routine.
[12/01/01] HJB raswin.c
Added include of langsel.h. Changed font of command window to ANSI
character set. Changed most messages to reference MsgStrs. Add
SwitchLang(English) calls for initialization to WinMain.
[12/01/01] HJB x11win.c
Restructured MenuItem and BarItem to make .text, .pos and .len
indirect, so that they can be fetched from MsgStrs, MsgAuxl and
MsgLens. The .pos field is used to specify the character offset
of the acceleration key. The main menu bar may now have non-zero
offsets. All the menu items have been changed to MsgStrs[StrM...]
referecences, and added include of langsel.h. Added ReDrawWindow
simply as a call to ReSizeWindow. This is overkill, but appropriate
for these infrequent calls.
[12/01/01] HJB tokens.h
Added tokens EnglishTok and SpanishTok.
[12/01/01] HJB graphics.h
Added prototype of ReDrawWindow, a system-dependent call to be used
after updating menus on language changes.
[12/01/01] HJB cmndline.c
Added include of langsel.h, changed prompts as follows:
"PDB file name:" MsgStrs[StrPrmtPDB]
"Image file name:" MsgStrs[StrPrmtImg]
"Molecule file name:" MsgStrs[StrPrmtMol]
[12/01/01] HJB tokens.c
Added the following tokens:
CADENA ChainTok
CADENAS ChainTok
DIBUJO CartoonTok
DIBUJOS CartoonTok
E AndTok
EJE AxesTok
EJES AxesTok
ELANCE BondTok
ELANCES BondTok
ENGLISH EnglishTok
ESQUELETO BackboneTok
ETIQUETA LabelTok
ETIQUETAS LabelTok
GIRO TurnTok
GIROS TurnTok
GRUPO GroupTok
HEBRAS StrandsTok
MOSTRAR DisplayTok
SALIR ExitTok
SPANISH SpanishTok
TODO AllTok
[26/12/99] HJB mswin31.c
Do not reset Voxel Data for each chain.
[02/10/99] HJB molecule.c
Update printer logic.
Changes from RasMol 2.7.0 to RasMol 2.7.1.1 include:
Introduction of a multilingual structure for RasMol.
Population of messages and menu lists for English and Spanish.
Upgrade of some of the Windows printer logic
Correction of coordinate handling for Mol2 and XYZ coordinates
Fix to the parsing of D2O.
The ability to automatically mark non bonded atoms in
wireframe and stick displays. Our thanks to R. Curtis Haltiwanger
for suggesting this change.
The ability to use a proportionally spaced font and to draw labels
with heavier strokes. Our thanks to Eric Martz for suggesting this change.
The ability to auto-recognize PDB vs. CIF and mmCIF datasets.
Extensive updating to the manual. Our thanks to William McClure,
Margaret Wong, Eric Martz and Frances Bernstein.
Updating the canvas title with the PDB ID code and EXPDTA information,
so models will be clearly distinguished from experimental data.
Our thanks to Helen Berman for suggesting this change.
The ability to report coordinates.
Additions to the list of pre-defined colours.
Improved accuracy of coordinates in pseudo-PDB output.
Fixes to the centering logic.
Changes from RasMol 2.7.0.1 to create RasMol 2.7.1:
[15/07/99] HJB documentation
Add Dunix binaries. Thanks to David Atkinson
[06/07/99] HJB all
Release 2.7.1
[05/07/99] HJB documentation
Cut-off date for Release 2.7.1 documentation changes.
[22/06/99] HJB all source
Cut-off date for Release 2.7.1 code changes.
[22/06/99] HJB command.c
Save fact that a data file was loaded inline. Add
processing for star command, all new options for
bondmode [all | none | not bonded ]
[22/06/99] HJB infile.c
Update DataFileFormat after autorecognition.
[22/06/99] HJB molecule.h
Add MarkAtoms to hold new bondmode flags.
[22/06/99] HJB pixutils.c, render.c
Add code for new star command.
[22/06/99] HJB script.c
Add logic to write star command output. Report data
loaded as CIF or as inline correctly. Warn users
that inline data is not being written out. Check
inversion of Y-axis on POVRAY3. Thanks to Curt
Haltiwanger for suggesting marking non-bonded atoms
on wireframe displays.
[22/06/99] HJB transfor.c
Add code for new star command, new bondmode options.
[18/06/99] HJB pixutils.h, pixutils.c
Change name of DisplayString to DisplayRasString to
avoid a conflict with X libraries. Add FontWid array
to hold character widths (FontSize for FS, FontSize/4
+1 + maximum x position for PS). Add FontStroke logic to
write cylinders instead of lines when FontStroke is not
zero.
[18/06/99] HJB render.c
Change name of DisplayString to DisplayRasString to
avoid a conflict with X libraries.
[18/06/99] HJB repres.c
When FonstStroke is non-zero, don't offset character
color by (ColourMask>>1), to allow room for color
adjustments in cylinder drawing.
[18/06/99] HJB script.c
Add logic to write PS flag for proportional spacing
on set fontsize, and logic to write set fontstroke n.
[18/06/99] HJB tokens.c, tokens.h
Add tokens for BlueTint (BlueTintTok), Brown (BrownTok),
FontStroke (FontStrokeTok), FS (FSTok), Gold (GoldTok),
Gray or Grey (GrayTok), GreenTint (GreenTintTok), HotPink
(HotPinkTok), Pick as an alternative for Picking
(PickingTok), Pink (PinkTok), PinkTint (PinktintTok),
SeaGreen (SeaGreenTok), SkyBlue (SlyBlueTok),
YellowTint (YellowTintTok)
[13/06/99] HJB command.c
Change processing of load inline command to work from
the currently opened script, saving the file position.
Accept HEADER and DATA_... as commands in a script,
processing that line and all subsequent lines as a
data file, unless a prior load inline command was already
done
[12/06/99] HJB infile.c
When processing a PDB file, test for DATA_... until
a non-comment, non-blank line is found. Revert
to CIF processing if DATA_... is found.
[11/06/99] HJB infile.c
In PDB format input extract EXPDTA for Info.technique.
In CIF format input accept _audit_block_code for the
entry ID, _exptl.method, _diffrn_radiation.probe or
_diffrn_radiation_probe for Info.technique. Preserve
low order bits of coordinates in xtrl, yrtl, ztrl. On
PDB output, report Info.technique in EXPDTA and reinsert
low-order bits for coordinates.
[10/06/99] HJB abstree.c
Add code to report coordinates for show selected cordinates
[10/06/99] HJB command.c
Recognize new commands, picking coordinates,
show selected cordinates. Update default title produced
by title command.
[10/06/99] HJB molecule.h
Add new Info fields for date and technique. Extend
identcode to 80 columns. Add CRD to Selection enum type.
Add prototype for ReviseTitle.
[10/06/99] HJB render.h, render.c
Add code to report coordinates for picking coordinates,
define PickCoord symbol.
[10/06/99] HJB tokens.h, tokens.c
Add code recognize COORD, COORDS, COORDINATE, COORDINATES for
new CoordTok, DATA_... for CIFDataTok, HEADER for HeaderTok
[09/06/99] HJB molecule.c
Put PDB entry ID and EXPDTA info into canvas title, report
EXPDTA data from Info.technique on reading file.
[06/06/99] HJB infile.c
Restore the origin on PDB and other outputs.
[06/06/99] HJB script.c
Change script output to include centering and
change various coordinate outputs to restore
origins the z-axis orientation.
[06/06/99] HJB command.c
Add command centre [CenX,CenY,CenZ] to center by offsets
from centre of gravity.
[03/06/99] HJB render.c
Remove call to TranslateToCentre, hold centering
in CenX, CenY and CenZ, decoupled from dials,
add RFRotate to ReDrawFlag on centering. Thanks to
Bohdan Schneider for pointing out the problems with
centering.
[03/06/99] HJB transfor.c
Remove TranslateToCentre, remove processing of CenX,
CenY and CenZ from dial values, and put it into
computation of ptr->x,y,z
Changes after release of RasMol_2.7.0.1:
[27/04/99] HJB README.html, Changelog.html, INSTALL.html, manual
Add navigation links at top and bottom of each page.
Add links for gzipped versions of raswin.hlp, rasmol.hlp.
Thanks to E. Martz and Kjeld Olesen.
[27/04/99] HJB INSTALL.html, manual
Replace empty copy of INSTALL.html in doc/, correct
embedded html in manual. Thanks to Kurt Giles.
Changes from RasMol_2.7.0 to create RasMol_2.7.0.1:
[22/04/99] HJB
Announce RasMol 2.7.0.1 on pdb-l@rcsb.org,
rasmol@lists.umass.edu, mmciflist@ndbdev.rutgers.edu
[11/04/99] HJB *.c, *.h
Update all comment blocks for new version and date
[11/04/99] HJB abstree.h
Realign Pred... to agree with ...Tok to correct
misaligned introduced by HJB (not AM) during merge of 2.6x1
into 2.7.0.
[11/04/99] HJB tokens.h
Fix definition of IsPredTok
[09/04/99] HJB molecule,h
Make residue identification case-insensitive.
Changes from RasMol_2.6.4, RasMol2.6x1 and RasMol_2.6_CIF.2 to
create RasMol_2.7.0:
[30/03/99] HJB all
Cleanup and release of version 2.7.0
[23/03/99] HJB abstree.c
Add code to select on alternate conformers. Increase
accuracy of torsion angle calculation.
[23/03/99] HJB command.c, command.h
Make InitHelpFile generally available, change to
WriteString for reporting CisBondCutOff for use on mac,
report models on show selected.
[23/03/99] HJB rasmol.c, raswin.c, rasmac.c
Add suggestion for help notice to initial text lines.
[23/03/99] HJB script.c
In order to support mac introduce WriteBuffer and
change all fprintf(outFile, ... to WriteBuffer, provide
code from fisipl for Ramachandran printer plot. Handle
signs of torsion angles. Thanks to F. C. Bernstein.
[23/03/99] HJB tokens.h, tokens.c
Add RamPrintTok, RPP, RDF, etc., hook POVRAY3 to the
new POVray code.
[20/03/99] HJB *.h, *.c
In general, the RasMol_2.6_CIF.2 version was used as a base
and upgraded with the RasMol_2.6.4 changes. The exceptions
are below
[20/03/99] HJB infile.c
Cell parameters are read with the double routine ReadDecValue
from 2.6_CIF.2, rather than ReadValue2 from 2.6.4
Changes from RasMol_2.6 to create RasMol_2.6x1:
[15/2/98] AM abstree.c, abstree.h
Add PredCisBond, DescribeObj, CalcPhiAngle, CalcPsiAngle,
CalcOmegaAngle, shift torsion angle calculations 180
degrees.
[15/2/98] AM command.c
Add FindCisBonds, CisBondCutOff, show of selected chains,
groups, atoms, show and write of phi-psi angles
[15/2/98] AM molecule.h, molecule.c
Add CIS bond logic
[15/2/98] AM rasmol.h, rasmol.c
Add USE_FD_SET_TYPE option
[15/2/98] AM script.h, script.c
Add WritePhiPsiAngles, code for POV-Ray version 3
[15/2/98] AM tokens.h
Add CisBondedTok, RamachanTok, CisAngleTok, PhiPsiTok,
define PHIPSI, CISANGLE, RAMACHAN, CISBONDED
Changes from RasMol_2.6 to create RasMol_2.6.4:
[8/2/99] RS command.c, rasmol.c, scripts.c, rastxt.c, raswin.c
rasmac.c
Final fixup and release of version 2.6.4
[27/12/98] RS *.h, *.c
Remove all non-ANSI-C prototypes and ensure use of ( void )
for empty argument lists. Upgrade all procedure delcarations.
Convert to use of MSWIN.
[27/12/98] RS abstree.c
Redo torsion angel calculation.
[27/12/98] RS applemac.c
Convert to Apple's new routine names
[27/12/98] RS cmndline.c, cmndline.h
New routine for mouse, keyboard, dials
[27/12/98] RS command.c, command.h
Move routines for mouse, keyboard, dials to cmndline.c.
Redo ParseColour. Reorganize command parsing
[27/12/98] RS infile.c
Change references to MMIO to MMIOLIB. Pass fp and buffer
to FetchRecord as argument. Add ReadValue2, ProcessPDBBond,
ProcessPDBUnitCell. Fix recognition of END. Use
InvalidateCmndline and UnusedArgument. Write MODEL and
ENDMDL records when appropriate
[27/12/98] RS molecule.c
Reorganize FindResNo as a character-oriented search tree
Add Cache.
[27/12/98] RS rasmac.c
Convert to Apple's new routine names
[27/12/98] RS rastxt.c
New text-only main program
[27/12/98] RS repres.c
Add LabelTermnii
[27/12/98] RS tranfor.c
Add TranslateToCentre
[27/12/98] RS transfor.h
Reorganize the logic defining DefaultAmbient, making
the default value 0.4 instead of 0.6, except for E&S, which
is still .05.
[27/12/98] RS tokens.c
New routine for character-oriented search tree for tokens.
[01/08/97] RS infile.c
Decreased the maximum valid alpha carbon to alpha carbon
distance to 4.2 Angstroms from 7.0 Angstroms. Thanks to
Kostas Sfyrakis and Harren Jhoti.
[15/04/97] RS molecule.c repres.c
Fixed a bizarre feature in the OpenVMS compiler that complained
about "a=*b" as "=*" operator is an obsoltete form and may not
be portable. Special thanks to Remington Stone.
[28/11/96] RS rasmol.h rasmol.c
Several minor fixes to compile RasMol under VMS. Special
thanks to Adam Ralph (and CCP4).
Changes from RasMol_2.6_CIF(Rev 1) to create RasMol_2.6_CIF(Rev 2):
[24/2/99] HJB Release of RasMol_2.6_CIF(Rev 2) at
http://www/bernstein-plus-sons.com/software/rasmol
and announce to mailing lists.
[21/2/99] HJB cif.h
Add prototypes of cif_make_handle, cif_read_file,
cif_make_file, cif_save_character to avoid compiler warnings
[21/2/99] HJB cif_ctonum.c
Remove unneeded values.h
[21/2/99] HJB cif_ctonum.h
Correct prototype
[21/2/99] HJB infile.c
Add cif_ctonum.h, define LoadCIFMolecule prototype,
initialize ch, add return to avoid compiler warnings.
[21/2/99] HJB abstree.c, cif.c, cif_ctonum.c, command.c,
infile.c, molecule.c
Use string_case.h instead of for IBMPC,
VMS and APPLEMAC.
[21/2/99] HJB rasmol.h
Update version, add some definitions from R. Sayle's
2.6.4 in preparation for 2.7.0.
[21/2/99] HJB rasmac.c, rasmol.c, raswin.c
Update reported date on startup.
[21/2/99] HJB render.c
Add cif_fract.h to avoid compiler warnings.
[21/2/99] HJB string_case.c
Replace garbled version, provide string_case.h.
[21/2/99] HJB script.c
Initialize first, last, radius, to avoid compiler warnings
[21/2/99] HJB transfor.c
Initialize min and max to avoid compiler warnings.
[10/1/99] HJB Release of RasMol_2.6_CIF(Rev 1) at
http://www.bernstein-plus-sons.com/software/rasmol
and announce to mmCIF mailing list.
[9/1/99] HJB cif.c
Change toupper calls to ToUpper calls.
[8/1/99] HJB command.c
Add argument to CreateMoleculeBonds to force zapping
on connect.
[8/1/99] HJB infile.c
Log requested bonds which cannot be made in NullBonds
and report to users, add RightJustify to right-justify
residue names, recognize _atom_site_disorder_group
for small molecule alternate conformerse, recognize bonds
which don't have either atom names or atom numbers.
[8/1/99] HJB molecule.c
Add argument to CreateMoleculeBonds to force zapping
on connect.
[8/1/99] HJB molecule.h
Add argument to CreateMoleculeBonds to force zapping
on connect, add NullBonds to log requested bonds which
cannot be made.
[8/1/99] HJB mswin31.c
Use VERSION to construct window title.
[8/1/99] HJB outfile.c
Use VERSION to construct Postscript output file header.
[8/1/99] HJB rasmac.c
Use VERSION to report version on startup.
[8/1/99] HJB rasmol.c
Use VERSION to report version on startup.
[8/1/99] HJB raswin.c
Use VERSION to report version on startup.
[8/1/99] HJB script.c
Use VERSION to construct various output file headers.
[8/1/99] HJB x11win.c
Use VERSION to construct window title.
Changes from RasMol_2.6 to create RasMol_2.6_CIF:
[22/12/98] HJB Preliminary release of RasMol_2.6_CIF at
http://www.bernstein-plus-sons.com/software/rasmol
[19/12/98] HJB command.c
correct handling of internal help files under windows,
and allow for unix help files on a mac.
[18/12/98] HJB Makefile.in, Imakefile
Update for CIF support.
[09/12/98] HJB infile.c
Cummulative changes for fractional coordinates,
CIF.
[09/12/98] HJB command.c
Changes for alt, model labels, colour schemes,
CIF.
[09/12/98] HJB molecule.h
Cummulative changes for fractional coordinates,
new colour schemes, CIF.
[09/12/98] HJB molecule.c
Cummulative changes for fractional coordinates,
new colour schemes, CIF.
[09/12/98] HJB x11win.c
Update comments, menus and version text.
[09/12/98] HJB mswin31.c
Update comments, output file commentary.
[09/12/98] HJB outfile.c
Update comments, output file commentary.
[09/12/98] HJB script.c
Update comments, output file commentary.
[09/12/98] HJB rasmol.c
Update comments, output file commentary.
[04/12/98] HJB pixutils.c
Update comments, code to stripe bonds for alternate
conformers.
[04/12/98] HJB pixutils.h
Update comments, protytpes to stripe bonds for alternate
conformers.
[04/12/98] HJB rasmac.c
Update comments, adjust code for current Metrowerks
compiler.
[04/12/98] HJB raswin.c
Update comments, adjust code for current Metrowerks
compiler.
[04/12/98] HJB tokens.h
Update comments, tokens for alt, model colours.
[04/12/98] HJB transfor.c
Update comments, add code for alt, model colours.
[04/12/98] HJB transfor.h
Update comments, prototypes for alt, model colours.
[23/11/98] HJB abstree.c
Add code for %A, %M specifiers, divide u/l case.
[22/11/98] HJB cif_fract.c
New routine, derived from cif2pdb by H.J. Bernstein
and F. C. Bernstein.
[22/11/98] HJB cif_fract.h.
New header for cif_fact.c.
[22/11/98] HJB cif_stx.c
New routine, derived from P. Ellis CBFlib parser.
[23/11/98] HJB render.c
Update comments, add code to stripe bonds for alternate
conformers.
[23/11/98] HJB repres.c
Update comments, add code to stripe bonds for alternate
conformers.
[09/09/98] HJB cif_ctonum.c
New routine, derived from ciftbx by S. R. Hall
and H. J. Bernstein.
[09/09/98] HJB cif_ctonum.h
New header for cif_ctonum.c.
[18/08/98] HJB cif.h
New header for cif.c, derived from CBFlib by P. Ellis
and H. J. Bernstein.
[18/08/98] HJB cif.c
New routine derived from CBFlib by P. Ellis and
H. J. Bernstein.
[14/08/98] HJB rasmol.c
Added hooks for termio for Linux. These changes
are similar to, but not identical to the FreeBSD hooks.
See the linux conditionals. -- H. J. Bernstein
Other Changes
The complete version 2 change history is in the directory ChangeLog
Updated 14 May 2011.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
rasmol-2.7.6.0/ChangeLog.txt 0000664 0000000 0000000 00000251602 13364034342 0015561 0 ustar 00root root 0000000 0000000 ChangeLog
RasMol 2.7.5.2
* RasMol Latest Windows * RasMol 2.7.5.2 Windows
Installer Installer
* RasMol Latest Source * RasMol 2.7.5.2 Source
Tarball RasMol Tarball
* RasMol Latest Manual * RasMol 2.7.5 Manual
* Donate to Support RasMol * Donate to Support RasMol
* Register your RasMol * Register your RasMol
Molecular Graphics Visualisation Tool
13 June 2009 (rev. 13 May 2011)
Based on RasMol 2.6 by Roger Sayle
Biomolecular Structures Group, Glaxo Wellcome Research & Development, Stevenage,
Hertfordshire, UK
Version 2.6, August 1995, Version 2.6.4, December 1998
Copyright (c) Roger Sayle 1992-1999
and Based on Mods by
+------------------------------------------------------------------------------+
| Author | Version, Date | Copyright |
|-------------------+----------------------+-----------------------------------|
| Arne Mueller | RasMol 2.6x1 May | (c) Arne Mueller 1998 |
| | 1998 | |
|-------------------+----------------------+-----------------------------------|
| Gary Grossman and | RasMol 2.5-ucb | (c) UC Regents/ModularCHEM |
| Marco Molinaro | November 1995 | Consortium 1995, 1996 |
| | RasMol 2.6-ucb | |
| | November 1996 | |
|-------------------+----------------------+-----------------------------------|
| Philippe Valadon | RasTop 1.3 August | (c) Philippe Valadon 2000 |
| | 2000 | |
|-------------------+----------------------+-----------------------------------|
| Herbert J. | RasMol 2.7.0 March | (c) Herbert J. Bernstein |
| Bernstein | 1999 | 1998-2011 |
| | RasMol 2.7.1 June | |
| | 1999 | |
| | RasMol 2.7.1.1 | |
| | January 2001 | |
| | RasMol 2.7.2 August | |
| | 2000 | |
| | RasMol 2.7.2.1 April | |
| | 2001 | |
| | RasMol 2.7.2.1.1 | |
| | January 2004 | |
| | RasMol 2.7.3 | |
| | February 2005 | |
| | RasMol 2.7.3.1 Apr | |
| | 06 | |
| | RasMol 2.7.4 Nov 07 | |
| | RasMol 2.7.4.1 Jan | |
| | 08 | |
| | RasMol 2.7.4.2 Mar | |
| | 08 | |
| | RasMol 2.7.5 Jun 09 | |
| | RasMol 2.7.5.1 Jul | |
| | 09 | |
| | RasMol 2.7.5.2 May | |
| | 11 | |
+------------------------------------------------------------------------------+
This Release by
Herbert J. Bernstein, Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
yaya@bernstein-plus-sons.com
Copyright (c) Herbert J. Bernstein 1998-2009
----------------------------------------------------------------------
IMPORTANT
This version is based directly on RasMol 2.7.5.1, RasMol 2.7.4.2, RasMol
2.7.4.1, RasMol 2.7.4, RasMol 2.7.3.1, RasMol 2.7.3, RasMol 2.7.2.1.1 and
on RasMol 2.7.2, on RasMol 2.7.1.1, on RasTop 1.3, on RasMol version
2.6_CIF.2, on RasMol version 2.6x1, on RasMol version 2.6.4, and RasMol
2.5-ucb and 2.6-ucb. Please read the file NOTICE for important notices
which apply to this package and for license terms (GPL or RASLIC).
This version of RasMol is not in the public domain, but it is given freely
to the community in the hopes of advancing science. If you make changes,
please make them in a responsible manner, and please offer us the
opportunity to include those changes in future versions of RasMol.
----------------------------------------------------------------------
Changes from RasMol 2.7.5.1 to RasMol 2.7.5.2 include:
* Faster surface rendering by use of NearTree 3.1
* Updates to GTK version from T. Ikonen
* Use of CBFlib 0.9.2
* Use of CQRlib 1.1.2
* Minor bug fixes
Changes to RasMol 2.7.5.1 to create RasMol 2.7.5.2:
[24/04/2011] HJB command.c, command.h, molecule.c, molecule.h
Add time command, remove redundant tree builds.
Change flags to NearTree 3.1 interface
[13/12/2009] TPI render.c
PickAtoms(): Use WriteMsg() for text output
DescribeAtom(), PickAtoms(): Reindent
[13/12/2009] TPI gtkwin.c
UpdateScrollBars(): Do not set ReDrawFlag.
Fix screen update on picking labels etc.
Remove unused variables, reindent.
[02/09/2009] HJB maps.c
Change maps to 4.5 sigma cutoff.
[02/09/2009] HJB cmndline.c, command.c
Correct failure to do world rotation in new mouse mode
[09/08/2009] HJB cmndline.c, command.c
Restore general mouse control of bond rotation lost in
2.7.4.2 to 2.7.5 transition
[23/07/2009] HJB maps.c
As per Marian Szebenyi correct the skip of symmetry
ops in CCP4 maps by missing factor of 80.
Changes from RasMol 2.7.4.2 to RasMol 2.7.5 include:
* Support for SBEVSL movie commands.
* Support for Lee-Richards surface approximation by contouring
pseudo-Gaussian electron densities.
* Selection of atoms by proximity to map contours
* Coloring of maps by the colors of neighboring atoms
* Signficant improvements to the GTK version by Teemu Ikonen
Changes to RasMol 2.7.4.2 to create RasMol 2.7.5.1:
[18/07/2009] HJB .symlinks
Update .symlinks to 2.7.5
[17/07/2009] HJB cif.c command.c raswin_install.nsi
Windows port changes: Update NSIS installer script
Change from mktemp to tmpfile and use rewind not freopen
[17/07/2009] HJB rasmol.doc rasmol.hlp rasmol.html cif.c command.c
rasmol.man rasmol.tex rasmol.vms raswin.rtf
Update doc for 2.7.5, and fix some spacing
[17/07/2009] HJB cif.c x11win.c
Correct X11 file menu for more than 5 open files
Correct cif_read_file CBFlib version to use a temporary file
[16/07/2009] HJB rasmol_install.sh
Correct reporting of font installs for Chinese.X and Japanese.X
[14/07/2009] HJB transfor.c
Fix missing scaling in new translate logic
[12/07/2009] HJB command.c command.h tokens.c trnasfor.c transfor.h
Preliminary movie play logic.
[11/07/2009] HJB command.c
Switch record templates to SSSSSS as per manual
Fix a bug in defer symbol linking
Report undefined symbols in calls to show defer symbol
[10/07/2009] HJB Imakefile_base command.c
Correct Imakefile_base
Add defer/execute movie interaction
[09/07/2009] HJB Imakefile_base rasmol_build_options.sh
Provide new script, rasmol_build_options.sh to reconstruct
new Imakefile from stable Imakefile_base
[09/07/2009] HJB Imakefile rasmol.c
Default Imakefile to use local copies of CQRLIB, CVECTOR,
XFORMSLIB and CBFLIB.
Change from use of fl_init to fl_initialize for xforms-1.0.91
[08/07/2009] HJB Imakefile abstree.c applemac.c cif.stx.tab.c cmndline.c
command.c command.h graphics.h gtkwin.c multiple.c
outfile.c rasmac.c rasmol.c rastxt.c raswin.c render.c
repres.c transfor.c transfor.h wbrotate.c wbrotate.h x11win.c
Partial changes for defer/execute command.
Update versions of external files used in Makefile.
Cleanup of varibables names for saving dial values.
[04/07/2009] HJB command.c maps.c molecule.c pixutils.c rasmol.h repres.c
transfor.c
Clean up errors in map color atom command and remove use
of polys with differing vertex colors by breaking up the
triangles into monchrome subtriangles
[02/07/2009] TPI molecule.c
Add #define _GNU_SOURCE to get the correct definition of basename()
[29/06/2009] HJB command.c
Fix to map select atom add
Add esd to map show for distances to surfaces
and make code for distances to reentrant surfaces more accurate
[25/06/2009] HJB Imakefile command.c molecule.c molecule.h
Update to use of NearTree 2.1.2
Add code to report surface fit stats in map show
[18/06/2009] HJB Imakefile build_MACOSX.sh build_all.sh command.c
rasmol_install.sh tokens.c tokens.h
Add 'add' and 'within' parameters to map select atoms command
Also allow search radius to be specified
[16/06/2009] HJB Imakefile
Update Imakefile for use of installed packages
[14/06/2009] HJB Imakefile
Set up loads of necessary external packages from sourceforge
[13/06/2009] HJB Imakefile applemac.c cmndline.c cmndline.h command.c
graphics.h maps.h molecule.c molecule.h mswin31.c
multiple.c rasmac.c tokens.c tokens.h transfor.c transfor.h
x11win.c
Integrate surface and movie code with gtk code
[03/06/2009] TPI rasmol.c
DisplayUsage(): Revert back to fputs
[27/05/2009] TPI render.c
Do not assume sizeof(Pixel) == sizeof(Long)
Use variables of type Pixel consistently in buffer clearing functions.
Remove version of ClearBuffers() which does not require memset().
[17/07/2009] TPI graphics.h
add startup representation flags
[17/07/2009] HJB rasmol.doc rasmol.html rasmol.man,
Update manual to 2.7.5
[12/05/2009] TPI gtkwin.c
Fix vte input problems by using vte input callback instead of
g_io_watch.
Various file open fixes to GTK version
Fix setting of initial window size.
Fix file open in GTK version: Copy the file name to global var
DataFileName before calling FetchFile.
Add file type filtering to GTK filechooser.
Whitespace fixes.
[12/05/2009] TPI rasmol.c
Fix text output with VTE in GTK interface.
[12/05/2009] TPI command.c command.h rasmol.c
Refactor file opening code. Add support for opening more
than one file from the command line.
Simplify file opening code, remove globs and allow to open files
with spaces and other 'special' characters.
Fix reading files from stdin with '-' arg.
[07/02/2009] HJB command.c command.h rasmac.c rasmol.c rastxt.c raswin.c
tokens.c tokens.h transfor.c transfor.h
Updates to enable the record mode to files. Use with caution,
there are some problems with picking up ReDrawFlag on changes
in appearance. Mouse motion helps to get past the glitch.
[06/02/2009] HJB command.c command.h graphics.h gtkwinc. maps.c rasmac.c
rasmol.c rastxt.c raswin.c tokens.c tokens.h transfor.c
transfor.h
First pass at SBEVSL movie-making commands
[16/11/2008] HJB command.c maps.c
Update to Lee-Richards approximation for probe of given
probe radius with new logic for map spread 0; map scale off;
so that set radius ; map resolution .67; map spread 0;
map scale off; map generate surface produces a good surface
approximation
[20/05/2009] TPI molecule.c
ReviseTitle(): If no identcode, use filename in the title
[20/05/2009] TPI gtkwin.c multiple.c
Update GTK molecule list when a molecule is picked
gtkwin.c: set_gtk_open_file(); new function.
UpdateGtkMoleculeList(); free allocated lists, reindent
multiple.c: SelectMolecule(); call set_gtk_open_file()
[20/05/2009] TPI gtkwin.c rasmol.c
Fix recent files support in GTK version
build_gtkmenu(): Set recent user sort type to most recently used.
Display 30 recent files.
Reindent.
[20/05/2009] TPI printing-resolution.glade sizechooser.glade
Remove useless response_id properties from glade files
[18/05/2009] TPI gtkwin.c rasmol.c
Really fix VTE output in GTK version.
Stop using PTYs for terminal io with VTE.
Don't touch the controlling terminal during init and reset.
Make Delete key work and ignore unhandled terminal escape sequences.
Use custom versions of RasMolExit and RasMolFatalExit in GTK version.
Add some keyboard shortcuts to the GTK GUI.
[18/05/2009] TPI gtkwin.c
Change image export shortcut to C-X
[14/05/2009] TPI rasmol_48x48.xpm Imakefile gtkwin.c
Add an xpm icon for Rasmol.
Set window icon in the GTK version.
[13/05/2009] TPI command.c
revert the filename globbing and extension handling code
[15/02/2009] HJB rasmac.c rasmol.c raswin.c
Clean up handling of ReDrawFlag for appearance changes
[31/10/2008] HJB command.c maps.c
First pass a Lee-Richards surface approximation for map
generate with map resolution 1; map cale off; map level .5;
map generate mesh
Changes from RasMol 2.7.4.1 to RasMol 2.7.4.2 include:
* Alignment of command line sizing and positioning options for Windows
and X-Windows version. The command line options -height nnnn, -width
nnnn, -xpos nnnn and -ypos nnnn may be used to set the size and
position of the initial window.
* Change of the encoding for Japanese messages and menus from SJIS to
EUC-JP, and corrections to the fontset handling for Chinese and
Japanese. Thanks to Mamoru Yamanishi for contributing the improved
fontset logic.
* Updates to the rasmol_install.sh and rasmol_run.sh scripts to support
Chinese and Japanese using cxterm.
* Optional use of GTK. Thanks to Teemu Ikonen for the new GTK code.
Changes to RasMol 2.7.4 to create RasMol 2.7.4.1:
[18/03/2008] HJB graphics.h mswin31.c rasmol.c rastxt.c
raswin.c x11win.c
Add global InitWidth, InitHeight, InitXPos, InitYPos
to support common implementation of command line
options -height nnnn -width nnnn -xpos nnnn -ypos nnnn
to control initial window size and position
[18/03/2008] HJB x11win.c
Redo Japanese and Chinese fontset logic as per suggestion
by Mamoru Yamanishi
[18/03/2008] HJB Imakefile
Allow use of old X locale.
[18/03/2008] HJB langsel_unix.c
Switch Japanese for unix from SJIS to EUC-JP, introducing
langsel_unix.c
[21/02/2008] TPI actionmenu.gtk egg-macros.h eggfileformatchooser.c
eggfileformatchosser.h graphics.h gtkwin.c Imakefile
multiple.c printing-resolution.glade rasmol.c sizechooser.glade
transfor.c wbrotate.c
Addition of GTK interface by T. Ikonen, including new routines
actionmenu.gtk egg-macros.h eggfileformatchooser.c
eggfileformatchosser.h gtkwin.c printing-resolution.glade
sizechooser.glade
Changes from RasMol 2.7.3 to RasMol 2.7.4.1 include:
* Support for maps.
* Message and menu translations for Russian, Bulgarian, Japanese and
Chinese. Our thanks to G. Pozhvanov, G. Todorov, Nan Jia, Mamoru
Yamanishi and Katajima Hajime.
* Fix torsion angle calculation as per bug report and patch by Swati
Jain.
* Corrections by Ladislav Michnovic to port to more platforms.
* Code to read remediated PDB entries as suggested by Huanwang Yang
* Updated icons.
* Extended export menus.
Changes to RasMol 2.7.4 to create RasMol 2.7.4.1:
[19/01/2008] HJB
Release 2.7.4.1 created
[18/01/2008] HJB command.c, maps.c, maps.h, molecule.c
mswin31.c outfile.c outfile.h pixutils.c pixutils.h
rasmac.c, repres.c
Add LoadCCP4MapFile. Extend range of stereo angle to
60 degrees. Add GM notoggle command. Add code to
avoid trying to reuse a zapped map. Increase default
map resolution to 1 Angstrom. Change mapdata to
void * and use memmove to allow multiple data types,
add fields for number of grid divisions, map type,
element size and element type. Add code to load
and save maps in CBFlib format. Fix stereo.
[16/01/2008] HJB vector.c wbrotate.c
Fix multiple definitions of PI.
[14/01/2008] LM infile.c
Add include of string.h as per Ladislav Michnovic.
[14/12/2008] HJB graphics.h
Add buffers for slab and depth pixel-by-pixel
cutoff values.
[10/12/2007] GM langsel.c langsel.h languages/README.txt
languages/genlanselall languages/langsel*.utf.c,
tokens.c tokens.c
Corrected japanese langsel encoding. It is now
Shift_JIS.Added messages for NoToggle and ColourMode
commands. Updated langsel README.txt. Add NoToggle
and ColourMode commands
[06/12/2008] GM command.h
Add NoToggle and ColourMode variables.
[25/11/2007] HJB cif_fract.c
Rewrite calculation of matrix inverse.
Changes to RasMol 2.7.3.1 to create RasMol 2.7.4:
[19/11/2007] HJB
Release 2.7.4 created
[19/11/2007] HJB abstree.c abstree.h
Break out element identification from GetElemNumber
into GetElemDescrNumber. Fix torsion angle calculation
as per bug report and patch by Swati Jain.
[19/11/2007] HJB applemac.c
Add code to make languages sticky. Add register and
donate menu items, make languages sticky and launch
browsers.
[19/11/2007] HJB cif_fract.c
Correct calculation of matrix transforming orthogonal
to fractional coordinates and rewrite matrix
transforming fractional to orthogonal.
[19/11/2007] HJB command.c command.h
Add code for map commands. Make CommandError accessible
from other routines. Add Raster3D write/save option.
Allow proberadius of 6 Angstroms. Add Bulgarian,
Chinese, Japanese and Russian commands. Allow
spacefill up to 12 Angstroms. Allow mirror and
rotate suboptions on write/save.
[19/11/2007] HJB font.h, graphics.h
Allow access to font parameters and support info
[19/11/2007] HJB Imakefile
Add use of CBFlib
[19/11/2007] HJB infile.c
Make sensitive to PDB version to allow for handling of
remediated files, based on changes suggested by
Huanwang Yang of the RCSB PDB in April 2007.
[19/11/2007] GT langsel.c languages/
langsel.c restructured to be generated from separate
language files in the directory languages/
[19/11/2007] HJB molecule.c molecule.h
Add atom type processing and DA, DC, DG, DT, DI for
remediated PDB DNAs, based on changes suggested by
Huanwang Yang of the RCSB PDB in April 2007.
[19/11/2007] HJB multiple.c multiple.h
Manage map data for multiple molecules. Increase the number
of molecules from 5 to 15. Increase the number of characters
in the name to 33 characters.
[03/12/2006] HJB outfile.c
Clean up compilation warnings in outfile.c
[19/11/2007] HJB outfile.c outfile.h
Add Raster3D support based on code by V. Stanev. Partial
Vector PS map support.
[19/11/2007] HJB pixutils.h
Fix stereo of ribbons and map surfaces. Protect against
duplicate definition of Knot struct. Make ClipPolygon
accessible.
[19/11/2007] HJB rasmac.c rasmac.h
Increase terminal window to 132 characters. Add About dialog.
Clean up maps on exit. Add support for Russian, Bulgarian,
Chinese and Japonese. Add register and donate browser calls.
Add G4 CPU type. Extend export file types.
[19/11/2007] HJB RasMac.r
Update icons to new style. Extend Export menu to BMP...,
GIF..., IRIS RGB..., PPM..., Sun Raster, PostScript, PICT...,
Vector PS ..., Molscript ..., Kinemage ..., POVRay 3 ...,
VRML ..., Ramachandran ..., Raster3D ..., RasMol Script ....
Extend Apple menu to About RasMol..., RasMol Help ...,
Register ..., Donate ....
[19/11/2007] HJB rasmol.c
Update to release 2.7.4 with map support.
[19/11/2007] HJB script.c script.h
Add code to write out scripts for maps.
[19/11/2007] HJB string_case.c string_case.h
Fix case sensistive of last character comparison of strcasecmp and
strncasecmp. Add str255casecmp, strcasestr.
[19/11/2007] HJB tokens.c tokens.h
Add tokens for Average (MeanTok), Bulgarian (BulgarianTok),
Chinese (ChineseTok), Contour (ContourTok = LevelTok),
Generate (GenerateTok), Japanese (JapaneseTok), Level (LevelTok
= ContourTok), Map (MapTok), Mask (MaskTok), Mesh (WireframeTok),
Mirror (MirrorTok), New (NewTok), Next (NextTok), R3D or
Raster3D (Raster3DTok), Resolution (ResolutionTok), Spacing
(SpacingTok), Spread (SpreadTok), Width (SpreadTok),
[19/11/2007] HJB transfor.c transfor.h
Add map point colouring routines, ColourPointAttrib and
ColourPointPotential.
[19/11/2007] HJB x11win.c
Extend Export menu to BMP ..., GIF ..., IRIS RGB ..., PPM ...,
Sun Raster, PostScript, PICT ..., Vector PS ..., Molscript ...,
Kinemage ..., POVRay 3 ..., VRML ..., Ramachandran ...,
Raster3D ..., RasMol Script .... Enable and extend Help
menu to About RasMol..., User Manual..., Register...,
Donate.... Set locale for each langauge and use fontsets.
Use table of languages versus fonts in langsel. Add
About splash screen and revise popup logic to handle it.
Change text metrics to allow for Chineses and Japanese.
Try to make lack of access to shared memory non-fatal.
[03/10/2007] PK molecule.c
"RasMol - " string added to the title of the window.
[03/10/2007] PK multiple.c
Window title is updated when different molecule is selected.
[02/02/2007] HJB rasmol.c
Remove // comments for AIX build. Fix signed length conflict
[01/03/2007] GT rasmol.c
Chinese version.
[23/12/2006] HJB x11win.c
Detect remote X server that does not share memory
[29/12/2006] HJB rasmol.c x11win.c
Update x11win.c and rasmol.c to add links to list of browsers
and to kill About dialog when the menu bar is selected
[29/12/2006] HJB rasmol_install.sh
Update rasmol_install.sh to allow recompilation of fonts
on install to handle openwin and other old systems that
can't handle byte-swapped bdf files, and add enviroment
variable RASMOL_NOSPAWN to suppress spawn in intermediate
xterm from rasmol_run.sh. -- HJB
[23/12/2006] HJB rasmol_install.sh, rasmol_run.sh scripts
Add new rasmol_install.sh and rasmol_run.sh scripts
[29/11/2006] HJB raswin.idm
Fix missing raswin.idm in src.
[29/11/2006] HJB rasmol.c
Add missing include of sys/stat.h in rasmol.c
[10/12/2006] HJB x11win.c
Additional updates for linux build with Russian, cleaning
up X11 font selection for CP1251 and recovering when fonts
are missing. -- HJB
[03/12/2006] HJB x11win.c
Mods for about screen under Linux -- HJB
[28/11/2006] HJB x11win.c
Changes for Russian and About dialog in unix
[20/10/2006] HJB wbrotate.c
Localize " not found!" message in RemoveBond and CreateBondAxis
[16/09/2006] HJB x11win.c rasmol.c
Start of RasMol Russian Translation Project based on translations
by Gregory A. Pozhvanov of Saint Petersburg State University.
[11/02/2006] HJB script.c script.h
Add mirror and rotate options for VRML.
Changes from RasMol 2.7.2.1.1 (the final reference release of RasMol 2.7.2) to
RasMol 2.7.3.1 include:
* Adjustment to the mouse handling for a better, more natural feel. Our
thanks to C. Chigbo for the suggestion.
* Correction to cif.c for blanks after an initial quote mark.
* Correction to mswin31.c to restore lost initializations of ZRange and
DialValue[8..9].
* Modifications by Mamoru Yamanishi to Imakefile and rasmol.c to use
xforms for GUI file open. This patch needs the opens source xforms
1.0.90 library by Steve Lamont.
* Correction to molecule.c to correct input of xyz files. Thanks to
Stuart Prescott.
* Revision to CPK colors by C. Chigbo. The new colors are called CPKNEW.
The current CPK colors remain available as CPK.
* Correction to negative torsion angle monitors and to imprecise
distance and angle monitors by C. Chigbo. This patch corrects the
display of negative torsion angles caused by use of the unsigned short
type, and correctys imprecise distance and angle displays. This
extends the original patch which was just for torsion angles
(torsion.patch). A side effect of this change is to limit the
available range for distance monitors to approximately 327 AAngstroms.
* Initial code for display of solid Lee-Richards molecular surfaces.
This patch adds the basic code for display of Lee-Richards surfaces
with a new Molecular Surface menu item, and surface molecule and surface solvent commands.
* Corrections of ribbons 0, etc. commands by R. Chachra. With this
patch, the wireframe 0, ribbon 0, cartoon 0, backbone 0, strands 0 and
trace 0 commands work the same as these command with off instead of 0.
Changes to RasMol 2.7.3 to create RasMol 2.7.3.1:
[21/04/2006] HJB rasmol.h RasMac.r raswin.rc
Update version to 2.7.3.1
[21/04/2006] CC abstree.c render.c repres.c repres.h
Fix by Clarice Chigbo to improve accuracy of
distance calculations by changing from Long to
double. Report model number. Use Long instead
of short for monitors.
[15/12/2005] HJB x11win.c
Fix mouse runaway by removing conflict of HeldStep
and HeldButton variable name use.
[16/07/2005] HJB abstree.c infile.c render.c
Correct sign errors in use of ztrl
Changes to RasMol 2.7.2.1.1 to create RasMol 2.7.3:
[06/02/2005] HJB
Release 2.7.3 created
[21/01/2005] HJB molecule.c
Correct XYZ input by capping atom types. Thanks to
Stuart Prescott.
[16/01/2005] HJB applemac.c, cmndline.c, command.c, command.h,
infile.c, langsel.c, langsel.h, langsel_mac.c,
molecule.c, molecule.h, mswin31.c, multiple.c,
pixutils.c, pixutils.h, rasmac.c, rasmol.c,
rastxt.c, raswin.c, render.c, render.h, repres.c,
repres.h, tokens.c, tokens.h, transfor.h, x11win.c
Base level of changes for Lee-Richards molecular
surfaces.
[12/01/2005] Clarice Chigbo repres.c, render.c, repres.h
Correction to negative torsion angle monitors and to imprecise
distance and angle monitors; limits the available range for
distance monitors to approximately 327 Angstroms.
[17/01/2005] Clarice Chigbo script.c
Output CPKNEW in scripts
[04/01/2005] Ricky Chachra command.c
Fix to wireframe 0, ribbon 0, cartoon 0, backbone 0,
strands 0 and trace 0 commands to work the same as these
command with off instead of 0
[30/10/2004] Mamoru Yamanishi Imakefile, rasmol.c
Used xforms to provide GUI for file open under X-windows
[21/10/2004] Clarice Chigbo tokens.c, tokens.h
Define CPKNEW token
[20/10/2004] Clarice Chigbo transfor.c, transfor.h
New CPK color table
[26/04/2004] HJB cif.c
correction to handling of blank immediately following
initial quote mark.
[26/04/2004] HJB vector.c
correction to SubtractAtoms for bond rotation.
Changes from RasMol 2.7.1 (the final reference release of RasMol 2.7.2) to
RasMol 2.7.2.1.1 include:
* Post release patches to command.c were included to fix the handling of
load inline in the UCB multiple molecule environment. In addition
conditional code controlled by STRICT was disabled to restore
operation of load inline under windows. Thanks to Jan Reichert
for pointing out these problems. Thanks to E. Martz
for pointing out an error in the Spanish
translation credits which has been corrected. Thanks to a report by
Julien Hering, the omission of a prior fix to the MS Windows version
was found and corrected on 7 May 2004.
* Adaption of the multilingual mods from RasMol 2.7.1.1 into Rasmol
2.7.2.1.
* Rewrite of the mouse handling and rotation logic to correct the
problems in 2.7.2 and make the feel of 2.7.2.1 closer to that of
RasMol 2.7.1.
* Addition of French menus and messages
* Addition of Italian menus and messages
* Adoption of picking for selection of atoms, groups or chains from
RasTop 1.3.
* Adoption of backclipping from RasTop 1.3
* Adoption of shadepower command for glassy surfaces from RasTop 1.3
* Change of the menu stereo option to rotate cross-wall-none
* Allow longer atom names (12 characters) in CIFs.
* Incorporation of some of the code from the UCB RasMol variants. Out
thanks to Eileen Lewis and Marco Molinaro for their cooperation in
contributing the UCB Enhanced RasMol code for incorporation into the
RasMol 2.7 series.
* Code to represent bonds in and to alternate conformers with a narrowed
portion in the middle of each bond.
* An attempt to fix some of the chirality reversals in some of the
output modes.
* Fixes for some of the problems reported since the last release.
Post-release changes to RasMol 2.7.2.1.1:
[07/05/04] HJB mswin31.c
restored lost fix for intialization of ZRange and
DialValue[8..9] and rebuilt raswin.exe. Thanks to
Julien Hering.
[14/02/04] HJB pixutils.c
remove static from declaration of ClipVector.
[14/02/14] HJB cif_stx.c
remove trailing characters from #endif.
[03/02/04] HJB Makefile.in
Change transfer to transfor in 2 dependencies. Thanks
to R. Harlow.
Changes to RasMol 2.7.2.1 to create RasMol 2.7.2.1.1:
[26/01/04] HJB abstree.c
Fix warning on sprintf calls with unused args, match long
variables with %ld format descriptors.
[26/01/04] HJB cif.c
Add brackets to avoid compiler warnings on dangling elses.
Fix cif_lex to parse 'O''' correctly. Change from
WORD to CIFWORD to avoid conflict with windows.h.
[26/01/04] HJB cif.h
Change from WORD to CIFWORD to avoid conflict with windows.h.
Add prototype for cif_free_handle.
[26/01/04] HJB cif.stx.tab.c
Change from WORD to CIFWORD to avoid conflict with windows.h.
[26/01/04] HJB cif_ctonum.c
Remove unused variable dndec
[26/01/04] HJB cif_fract.c
Remove unused variable kk
[26/01/04] HJB cif_stx.c
Change from WORD to CIFWORD to avoid conflict with windows.h.
Add include of rasmol.h.
[26/01/04] HJB command.c
Initialize variables to avoid compiler warnings. Use %ld
format for long variables. Fix RotMode == RotBond which
should have been an assignment. Add parens on logical
expressions.
[26/01/04] HJB command.h
Add prototypes for ResumePauseCommand, InterruptPauseCommand.
[26/01/04] HJB graphics.h
Add include of windows.h
[26/01/04] HJB infile.c
Removed unused ReadValue2. Add brackets to avoid compiler
warnings on dangling elses. Initialize variables to avoid
compiler warnings.
[26/01/04] HJB langsel.c langsel_mac.c
Add include of string.h
[26/01/04] HJB molecule.c
Add include of graphics.h. Change to %ld format for longs.
Remove unused variables. Add brackets to avoid compiler warnings
on dangling elses.
[26/01/04] HJB molecule.h
Add prototype of TestDisulphideBridge.
[26/01/04] HJB multiple.c
Fix reversed comment terminator. Add include of string.h. Add
brackets to initializer to match structure.
[26/01/04] HJB multiple.h
Add prototype of ReRadius.
[26/01/04] HJB outfile.c
Initialize variables to avoid compiler warnings. Change to %ld
for long.
[26/01/04] HJB pixutils.c
Initialize variables to avoid compiler warnings. Removed unused
variables.
[26/01/04] HJB pixutils.h
Add prototypes of DrawTwinLine, ClipLine, ClipTwinLine,
ClipDashLine, DrawTwinVector, ClipVector, ClipTwinVector,
ClipDashVector.
[26/01/04] HJB rasmol.c
Add parens to avoid compiler warning.
[26/01/04] HJB rasmol.h
Set version and date. Add include of stdlib.h for malloc.
[26/01/04] HJB render.c
Change the handling of very long longs to avoid a compiler
warning. Use %ld format for longs.
[26/01/04] HJB repres.c
Remove unused variables. Use %ld format for longs. Initialize
variables to avoid compiler warnings.
[26/01/04] HJB repres.h
Add prototype of LoadDotsFile.
[26/01/04] HJB script.c
Add include of string.h. Use %ld format for longs. Initialize
variables to avoid compiler warnings. Remove unused variables.
Fix sign of trailing bits on VRML z coordinates.
[26/01/04] HJB script.h
Add prototype of WritePOVRay3File.
[26/01/04] HJB tokens.h
Add parens in definition of IsImageToken.
[26/01/04] HJB transfor.c
Add parens for logical expression. Remove unused variables.
Initialize variables to avoid compiler warnings.
[26/01/04] HJB transfor.h
Add prototype of DefineShade, RMat2RV, RV2RMat.
[26/01/04] HJB wbrotate.c
Add include of cmndline.h. Remove unused variables. Initialize
variables to avoid compiler warnings. Use %ld format for longs.
Add value for a returns that need them.
[26/01/04] HJB x11win.c
Initialize variables to avoid compiler warnings. Add brackets to
avoid compiler warnings on dangling elses.
[14/04/02] HJB Imakefile
Update to allow scripts to make multiple pixel depths by
setting PIXELDEPTH to 8, 16 or 32 externally. Add default
flags for various HP architectures.
[13/04/02] HJB cif.c
Reduce warnings by casting uses of size_t.
[13/04/02] HJB cif_ctonum.c
Reduce warnings by casting to int for pointers indptr-test.
[13/04/02] HJB command.c
Reduce warnings by explicit use of long (rather than Long)
for fpos, and casting to size_t for comparisons, etc.
[13/04/02] HJB infile.c
In ProcessPDBBond, match types of srcatm and dstatom by
changing from int to Long, casting to size_t for
comparisons, etc.
[13/04/02] HJB molecule.c
Change MemSize from int to size_t.
[13/04/02] HJB rasmol.c
Change AdviseLen from int to size_t, change socket to xsocket,
change __hpux to HPUX_LEGACY
[13/04/02] HJB rasmol.h
Add HPUX_LEGACY for old style hpux select.
[13/04/02] HJB render.c
Make test of sizeof(Long) > 4 conditional on not defining
_LONGLONG. Make some changes from Long to long, etc.
[13/04/02] HJB x11win.c
Cast some pointer diffs to int, change some Long to long,
etc.
[29/06/01] HJB command.c
Correct logic for inline load of a new molecule from
data file treated as a script.
[21/04/01] HJB all
Fix credit for initial Spanish translation. Thanks to
E. Martz.
[19/04/01] HJB command.c
Post release fix to handling of load inline in
windows version due to problem with STRICT logic.
Thanks to Jan Reichert for pointing
out the problem.
[18/04/01] HJB command.c
Post release fix to handling of load inline in UCB
multiple molecule environment. Thanks to Jan
Reichert for pointing out the
problem.
Changes from RasMol 2.7.1.1 and 2.7.2 to create RasMol 2.7.2.1:
[14/04/01] HJB script.c
Correct error in writing scripts with partial use of spacefill.
Thanks to Steven Vik for reporting the
problem.
[14/04/01] HJB rasmol.doc, itasmol2721.hlp, esrasmol.html
Updated manuals for 2.7.2.1.
[02/04/01] HJB abstree.c, abstree.h
Increase space for atom names from 4 to 12 characters.
[02/04/01] HJB applemac.c
Add symbolic ZRange, add 2 dials. See [12/01/01] changes for langsel.
[02/04/01] HJB cmndline.c, cmndline.h
Reworked all exits on mouse motion processing to leave values
in DialValues or WRot..., etc depending on RotMode. Made HeldButton
a global for future reference.
[02/04/01] HJB command.c, rasmol.c, rasmac.c, raswin.c
Change stereo command to cycle cross-wall-none.
[02/04/01] HJB command.c, script.c, transfor.c
Rework output of rotation information.
[02/04/01] HJB infile.c
Increase limit on atom names for CIF from 4 to 12 characters.
[02/04/01] HJB langsel.c langsel_mac.c
Add French (thanks to Jean-Pierre Demailly
) and Italian (Giuseppe Martini
and Giovanni Paolella
with contributions by: A. Davassi, M. Masullo, C. Liotto, G. Paolella,
G. Martini. Adapt to 2.7.2 menu structure.
[02/04/01] HJB mswin31.c
Removed "Printing Completed" message.
[02/04/01] HJB multiple.c
Save DotPtr to fix misplaced dots in multiple molecules. Save
LastTX, LastTY, LastTZ, LocalRadius, ShiftS, XlateCen. Make
"Insufficient memory" message be language dependent
MsgStrs[StrMalloc]
[02/04/01] HJB outfile.c, pixutils.c, repres.c
Rework backclipping separating ZOffset from new DepthValue,
define BitBack
[02/04/01] HJB tokens.c
Added the following tokens relative to 2.7.2, includes tokens
added for 2.7.1.1:
ASSE AxesTok
ASSI AxesTok
CADENA ChainTok
CADENAS ChainTok
CATENA ChainTok
CATENE ChainTok
COPY CopyTok
DEPTH DepthTok
DIBUJO CartoonTok
DIBUJOS CartoonTok
E AndTok
EJE AxesTok
EJES AxesTok
ELANCE BondTok
ELANCES BondTok
ELICHE HelixTok
ENGLISH EnglishTok
ELICHE HelixTok
ESQUELETO BackboneTok
ETIQUETA LabelTok
ETIQUETAS LabelTok
ETICHETTA LabelTok
ETICHETTE LabelTok
FILODIFERRO WireframeTok
FILDIFERRO WireframeTok
FILI StrandsTok
FRENCH FrenchTok
GIRO TurnTok
GIROS TurnTok
GRUPO GroupTok
GRUPPO GroupTok
HEBRAS StrandsTok
IMAGE ImageTok
ITALIAN ItalianTok
MOSTRAR DisplayTok
NASTRO RibbonTok
NASTRI RibbonTok
PASTE PasteTok
POSITION PositionTok
RIEMPIMENTO SpacefillTok
SALIR ExitTok
SCHELETRO BackboneTok
SELECTION SelectionTok
SHADEPOWER ShadePowerTok
SPANISH SpanishTok
TODO AllTok
TUTTO AllTok
VIEW ViewTok
VIGNETTA CartoonTok
VISUALIZZA DisplayTok
[02/04/01] HJB transfor.c
Rework interaction of mouse, local rotation and world rotation
to make horizontal mouse motion of individual molecule rotate
horizontally even when outer world rotation creates a tilt.
Restores incremental mouse motion effects similar to what
was in effect for 2.7.1, but with world rotations. Reworked
RasTop centering to restore 2.7.2 behavior -- defaults to
center the new rotation on the screen.
[02/04/01] HJB several
Make dial indices symbolic.
[02/04/01] HJB wbrotate.c, wbrotate.h
Rework interaction of mouse and world rotation to make
horizontal mouse motion of individual molecule rotate horizontally
even when outer world rotation creates a tilt.
Changes adopted from RasTop 1.3 in creating RasMol 2.7.2.1:
Note: These mods do not reflect the complete source of RasTop 1.3.
[31/01/00] PV command.c
Added code for selecting atom areas with mouse: changed
PickAtom() function name in PickAtoms(); changed PicAtome
identifier in PickAtom; added function SelectArea()
and DisplayArea(); added code for command "select view"
[30/01/00] PV command.c
Added command "select view" and corresponding code,
which allows to select a part of a molecule based on screen display.
[16/01/00] PV cmndline.c
In PerformMouseFunc() corrected MM_CLIP to access clipping with
the mouse, added MM_DEPT to access backclipping (depth) with the mouse.
[16/01/00] PV transfor.h, transfor.c, token.h, token.c, script.c
Added ShadePower in DefineColourMap(), which brings some interesting
shade variations. Added ShadePowerTok and command "set shade x"
with x between -20 to 20.
[03/01/00] PV transfor.c
Fixed bug (and modified) function Power() to handle Specpower
[12/14/99] PV
Added variables ShiftS and UseAutoDepthCue that adjust DepthCue
with slabbing.
[14/12/99] PV transform.c
Added function CentreTransform() to either move the origin in the
molecule or move the molecule to the origin (origin = True ).
Added variables Cenx,y,z, which mesure distance centre-origin.
[29/09/99] PV molecule.c
Fixed bug in FindCisBonds() (no zeroing of last group cisbondflag);
Added ability to convert triple bond to single (CreateBondOrder())
[24/09/99] PV cmndline.c
Correlated mouse binding to global variable MouseMode.
Removed EnableMenus(state==1) in ResetCommandLine().
Fixed mouse binding with INVERT on y values.
Fixed bug on capture status on mouse-up. Added MM_PREV
to mouse binding for deselection. Fixed INVERT on y
value for mouseup.
[21/09/99] PV command.c, render.h, render.c, transfor.h, transfor.c
Added four new picking modes: select an atom: PickAtom; select
a group: PickGroup; select a chain: PickChain; modify bonding/add
multiple bonds: PickBond. Allowed picking parameter shift = -1
when Ctrl key is down to deselect an atom (a group, a chain)
from the current selection. [Note by HJB 02/04/01 -- The UCB
and 2.7.2 bond picking was used in 2.7.2.1 instead of the
RasTop version]
[22/09/99] PV abstree.h, abstree.c
First step for saving atomsets & identifiers in RasMol scripts
(SetSize to 100 and SymEntry and SymbolTable in header).
[21/09/99] PV cif.h
Fixed missing declaration of cif_parse in cif.h
[21/09/99] PV cmndline.c
In ProcessCharacter()) added ESC (0x1b) character to interrupt
script pausing.
[21/09/99] PV command.c
Changed output for one-letter-code sequence in series of 50
characters with a space each subgroup of 10.
[21/09/99] PV infile.c
Compiling problems with RasMol 2.7.1 files (VisualC++ 5.0)
- explicited all conversions long to short in infile.c /*casting*/
[21/09/99] PV pixutils.c
Compiling problems with RasMol 2.7.1 files (VisualC++ 5.0)
- fixed casting in drawstar() and clipstar() in pixutils.c
Set ARCSIZE to 32768 under MSWIN, allowing drawing cylinders with
radii up to 250 RasMol Units. Current implementation gives a maximum
of 75 RU at maximum zooming. Mac implementation should be verified.
[14/07/99] PV abstree.c transfor.c
(Adapted from RasTop 1.3) Added shortcuts for direct evaluations
of atomsets (BuildAtomSet(), SelectZoneExpr()).
[14/07/99] PV abstree.c, transfor.c
Added shortcuts for direct evaluations of atomsets (BuildAtomSet(),
SelectZoneExpr()); gain up to 15 seconds of computer time on very
large molecules.
[10/07/99] PV cif.c
Fixed memory allocation bug in cif_make_handle
Changes from RasMol 2.7.1 to create RasMol 2.7.2:
[28/08/00] HJB all
Updates to comments, resources, etc for preliminary testing
release.
[21/08/00] HJB abstree.c, abstree.h
Change type Atom to RAtom to avoid conflicts with X.
Offset all uses of xorg, yorg, zorg databse entried with
fxorg, fyorg, fzorg database entries for UCB bond
rotation. Change char* strings to unsigned char* strings
to allow for extra UCB Angstrom and degree symbols.
[21/08/00] HJB applemac.c
Change from use of toolbar settings to use of RotMode.
Add new "Settings" menu.
[21/08/00] HJB cmndline.c
Adapt GSG code from UCB mods for mouse moves, to make
the moves control bond rotation, molecule rotation, or
world rotation, but change from use of toolbar settings
to use of RotMode
[21/08/00] HJB command.c
Add new error message (ErrNoBond) for "Bond for rotation
not picked". Add new parameter for alternate conformer
bond waist radius. Adapt to fxorg, etc. offsets. Adapt
GSG UCB pick bond tool bar button to a command line
command. Add show centre, show rotation, show translation
and show zoom commands. Add bond, unbond commands.
Add rotate bond, rotate molecule, rotate all command.
[21/08/00] HJB command.h
Add space after "__huge"
[21/08/00] HJB font.h
Adapt GSG UCB mods characters for Angstrom and degree to be
additional symbols, not repalcements.
[21/08/00] HJB graphics.h
Add new redraw flag, "RFRotBond" to signal that a bond
rotation is involved, and add it to RFRotate, RFApply and
RFInitial. Add ZRange. Move main X window definitions
into this header to facilitate toolbar development.
[21/08/00] HJB infile.c, infile.h
Change all Atom types to RAtom. Add xorg, etc. offsets
on all coordinate calauclations. Move GroupPool definition
to header.
[21/08/00] HJB molecule.h and all referring files
Change type Atom to RAtom to avoid conflicts with X.
Add fxorg, fyorg, fzorg database entries for UCB bond
rotation offsets.
[21/08/00] HJB multiple.c
Remove all use of the toolbar, converting to menu.
Detect last element of file name string. Update VarList
for current variables. Change to ANSI C prototypes.
Move revised DrawMoleculeList from GSG's UCB toolbar.c
into multiple.c, but drop list only into MolName[].
[21/08/00] HJB wbrotate.c, wbrotate.h
Remove all use of the toolbar, converting to menu.
Change to ANSI C prototypes. Revise bond and world
rotation logic to use full rotation, nor increment,
for improved accuracy. Change Bond rotation logic to
preserve nesting of bonds without changing the original
coordinates. Add database of selected bonds and logic
to add bonds on the fly and remove them.
[21/08/00] HJB vector.c, vector.h
Change to ANSI C prototypes. Replace Vector and Matrix
with their array definitions for clarity.
[27/02/00] HJB transfor.c, transfor.h
Add alternate conformer bond radius to EnableWireFrame
[23/02/00] HJB infile.c
Fix *- for - typo in XYZ and MOL2 input of coordinates
[23/02/00] HJB molecule.c
Fix D2O to DOD mapping. Thanks to Brian W. Beck.
[23/02/00] HJB pixutils.c
New code for alternate conformer bonds.
[23/02/00] HJN raswin.c
Update WinMail entry to WINAPI
[29/01/00] HJB molecule.c
Comment out chain by chain reset of bonding to allow for
het groups after TER at expense of slower bonding.
[29/01/00] HJB mswin31.c
Update printer logic for modern windows specs.
[29/01/00] HJB rasmac.c
Fix reference of monaco font.
[15/07/99] HJB (for AR) raswin.c
Add check for \r. Thanks for Andrew Raine.
[15/07/99] RS raswin.c
Add .ML2 and .SY2 extensions for Sybyl and MOL2.
Changes adapted from UCB rasmol in creating RasMol 2.7.2:
Note: These mods do not reflect the complete source of UCB RasMol. In
particular toolbar.h and toolbar.c have not been used in this pass, and
the full source of UCB RasMol has not yet been recovered.
[30/11/95] GSG rasmac.c
Hide command window. Add help screen menu logic. Add hooks to
load multiple molecules. Add toolbar menu to Windows menu. Make
mouse moves control bond rotation, molecule rotation or world
rotation depending on tool bar button choices. Same for scroll
bars.
[29/11/95] GSG applemac.c
Change default background for printing to white.
Hook scroll bar H values to bond angle (BRotValue),
molecule rotation angle (DialValue[1]) or
world rotation angle (WRotValue[1]) depending on
toolbar settings. Hook scroll bar V values to
molecule rotation angle (DialValue[0]) or
world rotation angle (WRotValue[0]) depending on
tool bar settings. Allow file open when less than
MAX_MOLECULES molecules.
[21/08/00] GSG font.h
Add characters for Angstrom and degree as replacements
for vertical bar and tilde.
[16/11/95] GSG render.c, render.h
Add PickBond. Add hooks to draw multiple molecules. Automatically
switch to the molecule of any picked atom. Add monitor for picked
distance, angle or torsion angle.
[14/11/95] GSG transfor.c
Add hooks for bond rotation and global rotation.
[14/11/95] GSG vector.c, vector.h, wbrotate.c, wbrotate.h
New routines introduced with UCB mods to allow for
bond rotations and global rotation.
[14/11/95] GSG infile.c
Add fxorg, fyorg, fxorg for MDL molecule input only.
[14/11/95] GSG molecule.c, molecule.h
Add fxorg, fyorg, fxorg and list of bonds to atom database
for world and bond rotation.
[11/11/95] GSG multiple.c, multiple.h
New routine introduced with UCB mods to allow for
multiple molecules.
[10/11/95] GSG tokens.c,tokens.h
Add MoleculeTok.
[10/11/95] GSG repres.h
Add flag for units to Monitors.
[09/11/95] GSG command.c, command.h
Add hooks for multiple molecules. Log background
status to allow default white print background.
Add molecule command.
[09/11/95] GSG rasmol.c
Add initialisation for multiple molecules.
Changes from RasMol 2.7.1 to create RasMol 2.7.1.1:
[21/01/01] FGR, HJB langsel.c, langsel_mac.c, mswin.c, applemac.c
Installed translations for Edit menu on mac and PC
provided by Fernando Gabriel Ranea.
[17/01/01] FGR, HJB langsel.c, langsel_mac.c
Corrections to translations by Fernando Gabriel Ranea, installed
by HJB with revisions to menu bar accelerators.
[12/01/01] HJB applemac.c
Added include of langsel.h. Added routine ReWriteStr255 to rewrite
menu bar items in place and tostr255 to convert other menu items
strings to Pascal form for use in SetmenuItemText. Set up
ReDrawWindow to refresh all menu strings and then redraw the menu
bar. Note that the rewrite of the main menu bar is _very_ risky
and may not survive system changes.
[12/01/01] HJB command.c
Added include of langsel.h. Remove redundant ErrorMsg array and Err...
definitions. Change messages to reference MsgStrs. Add English and
Spanish as commands calling SwitchLang.
[12/01/01] HJB infile.c
Fix coordinate typo in load of XYZ and Mol2 molecules.
[12/01/01] HJB langsel.c, langsel_mac.c, langsel.h
New routines to carry multi-lingual translations. Many thanks to
Fernando Gabriel Ranea for the bulk of the Spanish translations,
and for creating the initial Spanish version of RasMol 2.7.1. Note
that langsel.c uses the ANSI character set, while lansel_mac.c uses the
Macintosh character set.
[12/01/01] HJB molecule.c
Added include of langsel.h. Changed messages to reference MsgStrs.
Refixed D2O misparse, which had been previously fixed. Mod had been
lost.
[12/01/01] HJB mswin31.c
Added include of raswin.idm and langsel.h. Included partial update
to printer logic. Added ReDrawWindow as rewrite of menus with
ModifyMenu and RemoveMenu/AppendMenu calls.
[12/01/01] HJB rasmac.c
Added include of langsel.h. Added SwitchLang(English) calls
for initialization to main routine.
[12/01/01] HJB rasmol.c
Add fix for broken math routines by referencing atan2.
[12/01/01] HJB rasmol.h
Added include of langsel.h. Added SwitchLang(English) calls
for initialization to main routine.
[12/01/01] HJB raswin.c
Added include of langsel.h. Changed font of command window to ANSI
character set. Changed most messages to reference MsgStrs. Add
SwitchLang(English) calls for initialization to WinMain.
[12/01/01] HJB x11win.c
Restructured MenuItem and BarItem to make .text, .pos and .len
indirect, so that they can be fetched from MsgStrs, MsgAuxl and
MsgLens. The .pos field is used to specify the character offset
of the acceleration key. The main menu bar may now have non-zero
offsets. All the menu items have been changed to MsgStrs[StrM...]
referecences, and added include of langsel.h. Added ReDrawWindow
simply as a call to ReSizeWindow. This is overkill, but appropriate
for these infrequent calls.
[12/01/01] HJB tokens.h
Added tokens EnglishTok and SpanishTok.
[12/01/01] HJB graphics.h
Added prototype of ReDrawWindow, a system-dependent call to be used
after updating menus on language changes.
[12/01/01] HJB cmndline.c
Added include of langsel.h, changed prompts as follows:
"PDB file name:" MsgStrs[StrPrmtPDB]
"Image file name:" MsgStrs[StrPrmtImg]
"Molecule file name:" MsgStrs[StrPrmtMol]
[12/01/01] HJB tokens.c
Added the following tokens:
CADENA ChainTok
CADENAS ChainTok
DIBUJO CartoonTok
DIBUJOS CartoonTok
E AndTok
EJE AxesTok
EJES AxesTok
ELANCE BondTok
ELANCES BondTok
ENGLISH EnglishTok
ESQUELETO BackboneTok
ETIQUETA LabelTok
ETIQUETAS LabelTok
GIRO TurnTok
GIROS TurnTok
GRUPO GroupTok
HEBRAS StrandsTok
MOSTRAR DisplayTok
SALIR ExitTok
SPANISH SpanishTok
TODO AllTok
[26/12/99] HJB mswin31.c
Do not reset Voxel Data for each chain.
[02/10/99] HJB molecule.c
Update printer logic.
Changes from RasMol 2.7.0 to RasMol 2.7.1.1 include:
* Introduction of a multilingual structure for RasMol.
* Population of messages and menu lists for English and Spanish.
* Upgrade of some of the Windows printer logic
* Correction of coordinate handling for Mol2 and XYZ coordinates
* Fix to the parsing of D2O.
* The ability to automatically mark non bonded atoms in wireframe and
stick displays. Our thanks to R. Curtis Haltiwanger for suggesting
this change.
* The ability to use a proportionally spaced font and to draw labels
with heavier strokes. Our thanks to Eric Martz for suggesting this
change.
* The ability to auto-recognize PDB vs. CIF and mmCIF datasets.
* Extensive updating to the manual. Our thanks to William McClure,
Margaret Wong, Eric Martz and Frances Bernstein.
* Updating the canvas title with the PDB ID code and EXPDTA information,
so models will be clearly distinguished from experimental data. Our
thanks to Helen Berman for suggesting this change.
* The ability to report coordinates.
* Additions to the list of pre-defined colours.
* Improved accuracy of coordinates in pseudo-PDB output.
* Fixes to the centering logic.
Changes from RasMol 2.7.0.1 to create RasMol 2.7.1:
[15/07/99] HJB documentation
Add Dunix binaries. Thanks to David Atkinson
[06/07/99] HJB all
Release 2.7.1
[05/07/99] HJB documentation
Cut-off date for Release 2.7.1 documentation changes.
[22/06/99] HJB all source
Cut-off date for Release 2.7.1 code changes.
[22/06/99] HJB command.c
Save fact that a data file was loaded inline. Add
processing for star command, all new options for
bondmode [all | none | not bonded ]
[22/06/99] HJB infile.c
Update DataFileFormat after autorecognition.
[22/06/99] HJB molecule.h
Add MarkAtoms to hold new bondmode flags.
[22/06/99] HJB pixutils.c, render.c
Add code for new star command.
[22/06/99] HJB script.c
Add logic to write star command output. Report data
loaded as CIF or as inline correctly. Warn users
that inline data is not being written out. Check
inversion of Y-axis on POVRAY3. Thanks to Curt
Haltiwanger for suggesting marking non-bonded atoms
on wireframe displays.
[22/06/99] HJB transfor.c
Add code for new star command, new bondmode options.
[18/06/99] HJB pixutils.h, pixutils.c
Change name of DisplayString to DisplayRasString to
avoid a conflict with X libraries. Add FontWid array
to hold character widths (FontSize for FS, FontSize/4
+1 + maximum x position for PS). Add FontStroke logic to
write cylinders instead of lines when FontStroke is not
zero.
[18/06/99] HJB render.c
Change name of DisplayString to DisplayRasString to
avoid a conflict with X libraries.
[18/06/99] HJB repres.c
When FonstStroke is non-zero, don't offset character
color by (ColourMask>>1), to allow room for color
adjustments in cylinder drawing.
[18/06/99] HJB script.c
Add logic to write PS flag for proportional spacing
on set fontsize, and logic to write set fontstroke n.
[18/06/99] HJB tokens.c, tokens.h
Add tokens for BlueTint (BlueTintTok), Brown (BrownTok),
FontStroke (FontStrokeTok), FS (FSTok), Gold (GoldTok),
Gray or Grey (GrayTok), GreenTint (GreenTintTok), HotPink
(HotPinkTok), Pick as an alternative for Picking
(PickingTok), Pink (PinkTok), PinkTint (PinktintTok),
SeaGreen (SeaGreenTok), SkyBlue (SlyBlueTok),
YellowTint (YellowTintTok)
[13/06/99] HJB command.c
Change processing of load inline command to work from
the currently opened script, saving the file position.
Accept HEADER and DATA_... as commands in a script,
processing that line and all subsequent lines as a
data file, unless a prior load inline command was already
done
[12/06/99] HJB infile.c
When processing a PDB file, test for DATA_... until
a non-comment, non-blank line is found. Revert
to CIF processing if DATA_... is found.
[11/06/99] HJB infile.c
In PDB format input extract EXPDTA for Info.technique.
In CIF format input accept _audit_block_code for the
entry ID, _exptl.method, _diffrn_radiation.probe or
_diffrn_radiation_probe for Info.technique. Preserve
low order bits of coordinates in xtrl, yrtl, ztrl. On
PDB output, report Info.technique in EXPDTA and reinsert
low-order bits for coordinates.
[10/06/99] HJB abstree.c
Add code to report coordinates for show selected cordinates
[10/06/99] HJB command.c
Recognize new commands, picking coordinates,
show selected cordinates. Update default title produced
by title command.
[10/06/99] HJB molecule.h
Add new Info fields for date and technique. Extend
identcode to 80 columns. Add CRD to Selection enum type.
Add prototype for ReviseTitle.
[10/06/99] HJB render.h, render.c
Add code to report coordinates for picking coordinates,
define PickCoord symbol.
[10/06/99] HJB tokens.h, tokens.c
Add code recognize COORD, COORDS, COORDINATE, COORDINATES for
new CoordTok, DATA_... for CIFDataTok, HEADER for HeaderTok
[09/06/99] HJB molecule.c
Put PDB entry ID and EXPDTA info into canvas title, report
EXPDTA data from Info.technique on reading file.
[06/06/99] HJB infile.c
Restore the origin on PDB and other outputs.
[06/06/99] HJB script.c
Change script output to include centering and
change various coordinate outputs to restore
origins the z-axis orientation.
[06/06/99] HJB command.c
Add command centre [CenX,CenY,CenZ] to center by offsets
from centre of gravity.
[03/06/99] HJB render.c
Remove call to TranslateToCentre, hold centering
in CenX, CenY and CenZ, decoupled from dials,
add RFRotate to ReDrawFlag on centering. Thanks to
Bohdan Schneider for pointing out the problems with
centering.
[03/06/99] HJB transfor.c
Remove TranslateToCentre, remove processing of CenX,
CenY and CenZ from dial values, and put it into
computation of ptr->x,y,z
Changes after release of RasMol_2.7.0.1:
[27/04/99] HJB README.html, Changelog.html, INSTALL.html, manual
Add navigation links at top and bottom of each page.
Add links for gzipped versions of raswin.hlp, rasmol.hlp.
Thanks to E. Martz and Kjeld Olesen.
[27/04/99] HJB INSTALL.html, manual
Replace empty copy of INSTALL.html in doc/, correct
embedded html in manual. Thanks to Kurt Giles.
Changes from RasMol_2.7.0 to create RasMol_2.7.0.1:
[22/04/99] HJB
Announce RasMol 2.7.0.1 on pdb-l@rcsb.org,
rasmol@lists.umass.edu, mmciflist@ndbdev.rutgers.edu
[11/04/99] HJB *.c, *.h
Update all comment blocks for new version and date
[11/04/99] HJB abstree.h
Realign Pred... to agree with ...Tok to correct
misaligned introduced by HJB (not AM) during merge of 2.6x1
into 2.7.0.
[11/04/99] HJB tokens.h
Fix definition of IsPredTok
[09/04/99] HJB molecule,h
Make residue identification case-insensitive.
Changes from RasMol_2.6.4, RasMol2.6x1 and RasMol_2.6_CIF.2 to create
RasMol_2.7.0:
[30/03/99] HJB all
Cleanup and release of version 2.7.0
[23/03/99] HJB abstree.c
Add code to select on alternate conformers. Increase
accuracy of torsion angle calculation.
[23/03/99] HJB command.c, command.h
Make InitHelpFile generally available, change to
WriteString for reporting CisBondCutOff for use on mac,
report models on show selected.
[23/03/99] HJB rasmol.c, raswin.c, rasmac.c
Add suggestion for help notice to initial text lines.
[23/03/99] HJB script.c
In order to support mac introduce WriteBuffer and
change all fprintf(outFile, ... to WriteBuffer, provide
code from fisipl for Ramachandran printer plot. Handle
signs of torsion angles. Thanks to F. C. Bernstein.
[23/03/99] HJB tokens.h, tokens.c
Add RamPrintTok, RPP, RDF, etc., hook POVRAY3 to the
new POVray code.
[20/03/99] HJB *.h, *.c
In general, the RasMol_2.6_CIF.2 version was used as a base
and upgraded with the RasMol_2.6.4 changes. The exceptions
are below
[20/03/99] HJB infile.c
Cell parameters are read with the double routine ReadDecValue
from 2.6_CIF.2, rather than ReadValue2 from 2.6.4
Changes from RasMol_2.6 to create RasMol_2.6x1:
[15/2/98] AM abstree.c, abstree.h
Add PredCisBond, DescribeObj, CalcPhiAngle, CalcPsiAngle,
CalcOmegaAngle, shift torsion angle calculations 180
degrees.
[15/2/98] AM command.c
Add FindCisBonds, CisBondCutOff, show of selected chains,
groups, atoms, show and write of phi-psi angles
[15/2/98] AM molecule.h, molecule.c
Add CIS bond logic
[15/2/98] AM rasmol.h, rasmol.c
Add USE_FD_SET_TYPE option
[15/2/98] AM script.h, script.c
Add WritePhiPsiAngles, code for POV-Ray version 3
[15/2/98] AM tokens.h
Add CisBondedTok, RamachanTok, CisAngleTok, PhiPsiTok,
define PHIPSI, CISANGLE, RAMACHAN, CISBONDED
Changes from RasMol_2.6 to create RasMol_2.6.4:
[8/2/99] RS command.c, rasmol.c, scripts.c, rastxt.c, raswin.c
rasmac.c
Final fixup and release of version 2.6.4
[27/12/98] RS *.h, *.c
Remove all non-ANSI-C prototypes and ensure use of ( void )
for empty argument lists. Upgrade all procedure delcarations.
Convert to use of MSWIN.
[27/12/98] RS abstree.c
Redo torsion angel calculation.
[27/12/98] RS applemac.c
Convert to Apple's new routine names
[27/12/98] RS cmndline.c, cmndline.h
New routine for mouse, keyboard, dials
[27/12/98] RS command.c, command.h
Move routines for mouse, keyboard, dials to cmndline.c.
Redo ParseColour. Reorganize command parsing
[27/12/98] RS infile.c
Change references to MMIO to MMIOLIB. Pass fp and buffer
to FetchRecord as argument. Add ReadValue2, ProcessPDBBond,
ProcessPDBUnitCell. Fix recognition of END. Use
InvalidateCmndline and UnusedArgument. Write MODEL and
ENDMDL records when appropriate
[27/12/98] RS molecule.c
Reorganize FindResNo as a character-oriented search tree
Add Cache.
[27/12/98] RS rasmac.c
Convert to Apple's new routine names
[27/12/98] RS rastxt.c
New text-only main program
[27/12/98] RS repres.c
Add LabelTermnii
[27/12/98] RS tranfor.c
Add TranslateToCentre
[27/12/98] RS transfor.h
Reorganize the logic defining DefaultAmbient, making
the default value 0.4 instead of 0.6, except for E&S, which
is still .05.
[27/12/98] RS tokens.c
New routine for character-oriented search tree for tokens.
[01/08/97] RS infile.c
Decreased the maximum valid alpha carbon to alpha carbon
distance to 4.2 Angstroms from 7.0 Angstroms. Thanks to
Kostas Sfyrakis and Harren Jhoti.
[15/04/97] RS molecule.c repres.c
Fixed a bizarre feature in the OpenVMS compiler that complained
about "a=*b" as "=*" operator is an obsoltete form and may not
be portable. Special thanks to Remington Stone.
[28/11/96] RS rasmol.h rasmol.c
Several minor fixes to compile RasMol under VMS. Special
thanks to Adam Ralph (and CCP4).
Changes from RasMol_2.6_CIF(Rev 1) to create RasMol_2.6_CIF(Rev 2):
[24/2/99] HJB Release of RasMol_2.6_CIF(Rev 2) at
http://www/bernstein-plus-sons.com/software/rasmol
and announce to mailing lists.
[21/2/99] HJB cif.h
Add prototypes of cif_make_handle, cif_read_file,
cif_make_file, cif_save_character to avoid compiler warnings
[21/2/99] HJB cif_ctonum.c
Remove unneeded values.h
[21/2/99] HJB cif_ctonum.h
Correct prototype
[21/2/99] HJB infile.c
Add cif_ctonum.h, define LoadCIFMolecule prototype,
initialize ch, add return to avoid compiler warnings.
[21/2/99] HJB abstree.c, cif.c, cif_ctonum.c, command.c,
infile.c, molecule.c
Use string_case.h instead of for IBMPC,
VMS and APPLEMAC.
[21/2/99] HJB rasmol.h
Update version, add some definitions from R. Sayle's
2.6.4 in preparation for 2.7.0.
[21/2/99] HJB rasmac.c, rasmol.c, raswin.c
Update reported date on startup.
[21/2/99] HJB render.c
Add cif_fract.h to avoid compiler warnings.
[21/2/99] HJB string_case.c
Replace garbled version, provide string_case.h.
[21/2/99] HJB script.c
Initialize first, last, radius, to avoid compiler warnings
[21/2/99] HJB transfor.c
Initialize min and max to avoid compiler warnings.
[10/1/99] HJB Release of RasMol_2.6_CIF(Rev 1) at
http://www.bernstein-plus-sons.com/software/rasmol
and announce to mmCIF mailing list.
[9/1/99] HJB cif.c
Change toupper calls to ToUpper calls.
[8/1/99] HJB command.c
Add argument to CreateMoleculeBonds to force zapping
on connect.
[8/1/99] HJB infile.c
Log requested bonds which cannot be made in NullBonds
and report to users, add RightJustify to right-justify
residue names, recognize _atom_site_disorder_group
for small molecule alternate conformerse, recognize bonds
which don't have either atom names or atom numbers.
[8/1/99] HJB molecule.c
Add argument to CreateMoleculeBonds to force zapping
on connect.
[8/1/99] HJB molecule.h
Add argument to CreateMoleculeBonds to force zapping
on connect, add NullBonds to log requested bonds which
cannot be made.
[8/1/99] HJB mswin31.c
Use VERSION to construct window title.
[8/1/99] HJB outfile.c
Use VERSION to construct Postscript output file header.
[8/1/99] HJB rasmac.c
Use VERSION to report version on startup.
[8/1/99] HJB rasmol.c
Use VERSION to report version on startup.
[8/1/99] HJB raswin.c
Use VERSION to report version on startup.
[8/1/99] HJB script.c
Use VERSION to construct various output file headers.
[8/1/99] HJB x11win.c
Use VERSION to construct window title.
Changes from RasMol_2.6 to create RasMol_2.6_CIF:
[22/12/98] HJB Preliminary release of RasMol_2.6_CIF at
http://www.bernstein-plus-sons.com/software/rasmol
[19/12/98] HJB command.c
correct handling of internal help files under windows,
and allow for unix help files on a mac.
[18/12/98] HJB Makefile.in, Imakefile
Update for CIF support.
[09/12/98] HJB infile.c
Cummulative changes for fractional coordinates,
CIF.
[09/12/98] HJB command.c
Changes for alt, model labels, colour schemes,
CIF.
[09/12/98] HJB molecule.h
Cummulative changes for fractional coordinates,
new colour schemes, CIF.
[09/12/98] HJB molecule.c
Cummulative changes for fractional coordinates,
new colour schemes, CIF.
[09/12/98] HJB x11win.c
Update comments, menus and version text.
[09/12/98] HJB mswin31.c
Update comments, output file commentary.
[09/12/98] HJB outfile.c
Update comments, output file commentary.
[09/12/98] HJB script.c
Update comments, output file commentary.
[09/12/98] HJB rasmol.c
Update comments, output file commentary.
[04/12/98] HJB pixutils.c
Update comments, code to stripe bonds for alternate
conformers.
[04/12/98] HJB pixutils.h
Update comments, protytpes to stripe bonds for alternate
conformers.
[04/12/98] HJB rasmac.c
Update comments, adjust code for current Metrowerks
compiler.
[04/12/98] HJB raswin.c
Update comments, adjust code for current Metrowerks
compiler.
[04/12/98] HJB tokens.h
Update comments, tokens for alt, model colours.
[04/12/98] HJB transfor.c
Update comments, add code for alt, model colours.
[04/12/98] HJB transfor.h
Update comments, prototypes for alt, model colours.
[23/11/98] HJB abstree.c
Add code for %A, %M specifiers, divide u/l case.
[22/11/98] HJB cif_fract.c
New routine, derived from cif2pdb by H.J. Bernstein
and F. C. Bernstein.
[22/11/98] HJB cif_fract.h.
New header for cif_fact.c.
[22/11/98] HJB cif_stx.c
New routine, derived from P. Ellis CBFlib parser.
[23/11/98] HJB render.c
Update comments, add code to stripe bonds for alternate
conformers.
[23/11/98] HJB repres.c
Update comments, add code to stripe bonds for alternate
conformers.
[09/09/98] HJB cif_ctonum.c
New routine, derived from ciftbx by S. R. Hall
and H. J. Bernstein.
[09/09/98] HJB cif_ctonum.h
New header for cif_ctonum.c.
[18/08/98] HJB cif.h
New header for cif.c, derived from CBFlib by P. Ellis
and H. J. Bernstein.
[18/08/98] HJB cif.c
New routine derived from CBFlib by P. Ellis and
H. J. Bernstein.
[14/08/98] HJB rasmol.c
Added hooks for termio for Linux. These changes
are similar to, but not identical to the FreeBSD hooks.
See the linux conditionals. -- H. J. Bernstein
Other Changes
The complete version 2 change history is in the directory ChangeLog
----------------------------------------------------------------------
| OpenRasMol | Copying and Distribution | Contents | Installation Instructions |
| Changes | Things To Do | Introduction | Source Code and Binaries |
| RasMol Manual | Spanish Translation of RasMol Manual | Italian Translation of
RasMol Help File |
| Donate to Support RasMol | Release README | Register your RasMol |
----------------------------------------------------------------------
Updated 14 May 2011.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com
rasmol-2.7.6.0/ChangeLog/ 0000775 0000000 0000000 00000000000 13364034342 0015012 5 ustar 00root root 0000000 0000000 rasmol-2.7.6.0/ChangeLog/ChangeLog.1 0000775 0000000 0000000 00000044327 13364034342 0016740 0 ustar 00root root 0000000 0000000 [08/10/93] RS molecule.c
Solved problem with protein hydrogen bonding, in PDB files
containing both protein and nucleic acid sequences.
[07/10/93] RS outfile.c
Corrected problem with compressed postscript output using
"colour" instead of "color" resulting in monochrome output.
[06/10/93] RS abstree.c rasmol.c render.c
Moved #include inside the #ifdef IBMPC to avoid
compilation errors on SUN 386is without stdlib.h!
[05/10/93] RS command.c abstree.c
Added support for negative residue numbers when specifing
single residue numbers and ranges of residues, and allow the
use of negative numbers in RasMol conditional expressions.
[05/10/93] RS rasmol.c molecule.h
Altered the main loop of RasMol and the way char arrays are
initialised in molecule.h to avoid compilation warnings with
SGI's cc compiler. Thanks to Lachlan Bell (lhb@seqnet.dl..).
[04/10/93] RS Makefile Imakefile
Added a comment to the Makefile to the effect that the Xinput
library is linked using -lXi instead of -lXinput on SGIs.
[01/10/93] RS molecule.c render.c
Modified bug in molecule.c that only created new groups or
chains at changes in PDB residue serial numbers. This caused
ribbon problems on some GAP3.pdb. Thanks to Andrew Coulson.
[29/09/93] RS molecule.c
Changed method for determining hydrogen bond offests for the
RasMol "colour hbond type" command to not use the residue
serial numbers found in the PDB file.
[29/09/93] RS molecule.c molecule.h render.c
Recorded breaks in protein backbone caused by large alpha
carbon separation to avoid drawing ribbon over chain breaks.
[27/09/93] RS x11win.c
Improved the scroll bars to allow the `button' to be dragged
by moving the mouse whilst a button is depressed.
[27/09/93] RS molecule.c
Added a flag to indicate the source of the current secondary
structure assignment used by the program, i.e PDB vs DSSP.
[27/09/93] RS rasmol.c raswin.c raswin.rc raswin.idm command.c transfor.c
Replaced "Ball & Wire" with "Ribbons" on the display menu
and improved the way representations are enabled and disabled.
[24/09/93] RS molecule.c tokens.h command.c
Modified LoadPDBMolecule to read the secondary structure
assignment records (HELIX and SHEET) and use these as default
secondary structure assignments when they are present. Added
the command "structure" to force the use of DSSP definitions.
[24/09/93] RS molecule.c
Optimised Implementation of Kabsch and Sander's algorithm to
determine beta sheet secondary structures, reducing time to
analyse GLS2 from over two hours to 7mins on a sun4.
[23/09/93] RS abstree.c
Modified EvaluateProperty to test amino acid properties by
using an array containing a bitvector of properties for each
amino acid. This is both faster and easier to maintain.
[23/09/93] RS molecule.c command.c tokens.h abstree.c abstree.h
Completed prototype beta sheet secondary structure
determination based upon the Kabsch and Sander's algorithm.
Added the predicate "sheet" for amino acids in ladders.
[23/09/93] RS molecule.c molecule.h transfor.c abstree.c
Added pyrrolidine carboxylic acid and hydroxyproline (and
ASX and GLX) to the list of recognised amino acids for
determining hydrogen bonding and structure determination.
[22/09/93] RS molecule.c molecule.h tokens.h command.c render.c
abstree.c
Corrected bug with RasMol that caused proteins with actyl
N-terminii not to be recognised as amino acid sequences.
Added the predicate "protein" which is the set "amino" and
the n-terminal acetic acid. Thanks to Andrew Coulson.
[21/09/93] RS transfor.c transfor.h
Solved remaining problems with huge proteins in RasWin.
[21/09/93] RS molecule.c
Improved the performance of (helix) secondary structure
determination, by ordering the h-bonds to reduce searching.
[21/09/93] RS molecule.c render.c render.h transfor.c command.c
Modified altered the "Boxing" algorithm used to determine
bonding to use the Shadow tracing hash table. This both
reduces memory and dramatically increases performance
(halving the time to read 2GLS from 43s to 21s on a sun4).
[17/09/93] RS molecule.c molecule.h command.c raswin.c
Solved (some) problems caused by reading in huge proteins
with more than 32767 atoms and bonds, and larger in diameter
than can be represented by 16 bit integers.
[17/09/93] RS render.c
Corrected more problems caused by integer overflow and the
division by zero errors when zooming Ribbon models in RasWin.
[15/09/93] RS command.c
Extended expression syntax to include numbers as primitive
expressions to specify a given residue sequence number. Hence
the "select 5,6" is equiavalent to "select resno=5,resno=6"
and "select 10-20" means "select (resno>=10) and (resno<=20)".
[14/09/93] RS render.c
Corrected problems caused by integer overflow and integral
type conversion warnings with Spline code when zooming.
[13/09/93] RS x11win.c rasmol.h
Added check to the X Window System MIT shared memory extension
to test if server is on the same host (bug in XShm?) and hence
made MITSHM enabled as the default option.
[13/09/93] RS render.c pixutils.c pixutils.h
Completed implementation of ribbons using a MolScript-like
Hermite spline through Carson's control points. Optimized
fixed point implementation and improved ribbon clipping.
[12/09/93] RS render.c transfor.c transfor.h command.c molecule.h
Added an optional width parameter to the "ribbons" command
to allow the user to define ribbon width at each residue
independently, allowing for example wider ribbons in helix.
[12/09/93] RS pixutils.c pixutils.h command.c tokens.h
Added the command "set strands " to allow the user to
globally modify the number strands in ribbon representations.
[29/08/93] RS pixutils.c render.c command.c tokens.h transfor.c
transfor.h
Added prototype support for the RasMol ribbon representation
based on a fixed number of straight strands through Carson's
control points (peptide plane miday between alpha carbons).
[26/08/93] RS raswin.c rasmol.c command.c
Changed the default colour scheme to CPK.
[26/08/93] RS molecule.c
Added support for saving the currently selected atoms and
their connectivity information in an alchemy format file.
[26/08/93] RS x11win.c
Increased the minimum width of the screen to avoid bug in
the X Scroll bar range checking and limit XRange to word
boundaries to solve shared memory bug on some machines.
[25/08/93] RS transfor.c
Changed type of OrigCX, OrigCY and OrigCZ to type Long to
prevent RasWin crashing when loading PDB files centered a
long way from the co-ordinate origin.
[25/08/93] RS x11win.c
Improved code for using MIT's shared memory extension. The
code now uses the XShmCreateImage call and destroys the shmid
to ensure that the shared memory is reclaimed when RasMol is
terminated. Thanks to Andre Beck.
[24/08/93] RS abstree.c
Extended the syntax of primitive atom expressions to allow
the user to select residues (groups) whose names contain non
alphabetic characters, such as digits. Hence the new syntax
allows expressions of the form [SO4]20 and [+U]*P
[24/08/93] RS molecule.c molecule.h render.c transfor.c abstree.c
Added code to determine hydrogen bonding between nucleic
acid residues in distrinct chains. Modified "set hbond
backbone" code, to only draw a single bond between sugar
phosphate backbones for each pair of nucleotides.
[23/08/93] RS transfor.c
Modified the way in which ScaleColourAttrib tries to allocate
the colour map. Now if there are no free shades, it attempts
to allocate as many close matches as possible.
[23/08/93] RS x11win.c
Improved the XInput extensions dials box handling code, to
explicitly check the number of Dials and LEDs present. This
avoids problems on some SGI dials boxes. Thanks to Nick Blom.
[20/08/93] RS molecule.c molecule.h
Added a backbone representation for nucleic acid structures
by connecting sugar phosphate P atoms of consecutive residues.
[20/08/93] RS command.c
Fixed bug caused by "UpdateScrollBars" being called by the
`rotate' command, even when not running interactively.
[20/08/93] RS molecule.c molecule.h tokens.h command.c abstree.c
abstree.h
Added complete code for Kabsch and Sander secondary structure
determination of alpha helices. Added predefined set "HELIX"
that contains all atoms contained in a alpha helix structure.
[19/08/93] RS command.c
Fixed bug in LoadScriptFile that assumed that it was being
called after parsing a command line, causing RasMol to crash
SGI machines that had ".rasmolrc" initialisation files. Thanks
to Peter Murray-Rust and special thanks to Tom Smith!
[19/08/93] RS transfor.c command.c
The restrict command (and hydrogen/hetero menu options) now
removes bonds connected to any removed atom ignoring the
bondmode setting. Isabelle Phan (phan@bioch.ox.ac.uk)
[19/08/93] RS raswin.c
Added Alchemy file type to the RasWin FileOpen dialog box.
[19/08/93] RS molecule.c
Imposed maximum backbone bond length of 7.00 Angstroms.
[18/08/93] RS rasmol.c raswin.c
Modified the actions performed by ReDrawFlag when no
molecule is loaded. This allows the background colour
to be changed before loading a molecule.
[18/08/93] RS x11win.c
Corrected a memory deallocation problem, caused by the
XDestroyImage freeing the current frame buffer. This has
caused numerous untracable errors in previous versions.
[18/08/93] RS abstree.c molecule.c
Added support for IUPAC hydrogen names "1H", "2H" etc...
[10/08/93] RS command.c transfor.c transfor.h molecule.c molecule.h
Added the "colour hbond type" command to enable hydrogen
bonds to be drawn in colours associated with their offsets.
[09/08/93] RS abstree.c abstree.h command.c tokens.h
Completely reorganised the classification of amino acids into
predefined sets. Added sets for "surface" and "buried", for
"small", "medium" and "large" and synonyms "positive" and
"negative" for "acidic" and "basic", the "charged" sets.
[05/08/93] RS molecule.c molecule.h command.c tokens.h
Added support for reading in Alchemy format data files, as
used by the popular PC and Mac program. Thanks to Steve Ludtke.
[05/08/93] RS rasmol.c raswin.c x11win.c mswin31.c command.c
Changed default value of ReDrawFlag to initially be zero
until the molecule is loaded. This corrects bug when the
dispatcher doesn't check stdin when no molecule loaded.
[03/08/93] RS raswin.c mswin31.c
Added Print option to the RasWin file menu to allow the
current image to be printed out using the MS Windows
printer drivers. Tested for Mono & Colour PostScript.
[03/08/93] RS abstree.c
Changed definition of the sets "hydrophobic" and "polar".
Glycine (GLY) is now considered a polar amino acid residue.
[03/08/93] RS rasmol.c x11win.c
Improved dispatch of pending X11 events [RasMol now processes
all X Events until quiescent]. Holding down scroll bar arrow
spins until mouse button released. Fixed server colour search
bug when not running interactively. Thanks to Doug Phillips.
[03/08/93] RS molecule.c
Modified the order in which molecules are internally stored
so saving PDB files preserves the correct atom ordering. Also
solved output chirality problems when INVERT is defined.
[03/08/93] RS outfile.c
Fixed bugs and improved performance of writing output files
under MS Windows caused by rounding when INVERT is defined.
[29/07/93] RS outfile.c
Fixed bug when generating 24bit Run Length Encoded sun
rasterfile format images, thanks to Doug Phillips. Fixed
Monochrome RLE PostScript bug, thanks to Andrew Coulson. Also
changed "64 idiv" to "-6 bitshift" to speed up PostScript.
[28/07/93] RS outfile.c outfile.h command.c rasmol.c raswin.c
Modified the PostScript output routines to include a run
length encoding (RLE) compression option (as default). This
has significantly reduced the size of output files from
several megabytes to a few hundred kilobytes per image.
[27/07/93] RS tokens.h command.c molecule.c molecule.h
Added functions to write out currently selected atoms to a
PDB file as viewed from the current rotation matrix. This
command doesn't output CONNECT, SSBOND or MASTER records
yet. May also add HELIX, TURN and SHEET records in future.
[27/07/93] RS mswin31.c
Corrected bug that resulted in the PixMap image of a molecule
persisting (being redrawn after expose events) after the
molecule has been `closed' or `zapped!'.
[26/07/93] RS !Defined macro "Long" in rasmol.h to be the 32bit
integer type on the current architecture. This should be
defined as long on all architectures except the 64bit
DEC Alpha.
[23/07/93] RS Imakefile
Created Imakefile to allow easy compilation on local machines
using the `xmkmf' command to generate Makefiles with the
appropriate parameters.
[21/07/93] RS bitmaps.h graphics.h transfor.c
Corrected compilation warnings generated by the Solaris v2.0
C Compiler due to default signed chars and ANSI C division.
[08/07/93] RS command.c tokens.h
Changed the way keywords are identified from searching a table
of binary search trees ordered by frequency, to binary search
of an initialised array by token length. This should reduce
both memory and processing time.
[08/07/93] RS abstree.h
Altered the syntax of primitive atom expressions to provide
better support for numeric chain identifiers using optional
colon before chain. CYS11:1 can be distinguished from CYS111!
[03/07/93] RS rasmol.h raswin.c rasmol.c render.c molecule.c
Added support for Dynamic Data Exchange (DDE) of RasMol
parameters and valuation data under MS Windows 3.1.
[02/07/93] RS molecule.c
Corrected a typographical error resulting in molecules being
drawn back to front. This produced images of molecules with
the wrong chirality. Thanks to Pedro Coutinho and Tom Smith.
[01/07/93] RS command.c molecule.c
Solved problems when reading in PDB files that contain no
atoms such as the documentation files cpk.pdb and shapely.pdb.
This allows colour masks to be stored in a separate PDB file
and preloaded before the main molecule. Thanks to Bob Strunz.
[01/07/93] RS graphics.h x11win.c
Added much better support for 24bit and 32bit XVisual display
types. This now permits the 8bit RasMol to run find an
appropriate visual on 24bit and 32bit screens. This solves
problems with obscure default visuals. Special thanks to
Jenny Barna.
[30/06/93] RS command.c abstree.c abstree.c
Implemented the "WITHIN" function in atom expressions. This
selects all atoms within a specified radius of a given set
of atoms (defined by an atom expression). This even permits
the WITHIN command to be used recursively.
[29/06/93] RS x11win.c
Improved the local colour map support for 8bit displays. The
program no detects if the entire global colour map is already
allocated and forces the use of a local colour map. This gets
around the problems of black on black menu bottons and scroll
bars.
[27/06/93] RS command.c transfor.c transfor.h
Implemented the "colour [atom] amino" command that colours
amino acid residues by their properties. These colours are
more intuitive (conventional) than shapely colours and better
for a range of displays. Thanks to Andrew Coulson.
[27/06/93] RS molecule.c transfor.c abstree.h abstree.c
Added much better support for a wide variety of element
types by introducing element handles. Van der Waals radii
and CPK colours are now maintained for a much larger number
of atom types.
[27/06/93] RS command.c render.c render.h transfor.c transfor.h
Implemented the "ssbond " and "hbond " commands
to represent hydrogen bonds and disulphide bridges as thick
cylinders as well as dashed vectors. Significantly altered
the dynamics of RasMol by making backbone, hbond and ssbond
selection lazy. All these modes always clip vectors and
cylinders. This'll speed up transformation and selection.
[27/06/93] RS rasmol.c raswin.c abstree.c abstree.h
Added predicates for "aliphatic" and "aromatic" predefined
sets. Separated expression handling from molecule.c
[27/06/93] RS command.c graphics.h x11win.c mswin31.c
Added the "hourglass" variable to rasmol, that enables and
disables the use of the hou glass cursor whilst RasMol is
busy drawing and image. This was infuriating during DDE.
[27/06/93] RS render.c pixutils.c
Implemented the section slabmode to draw only a two a cross
section on the current clipping plane. Modified the atom
picking to accept this mode, and fixed a minor bug in the
"half" and "solid" slabmodes for drawing and picking. Removed
clipping code from the shadowing scanline routine.
[24/06/93] RS outfile.c
Corrected problem when outputing postscript files. A rounding
error when shrinking a picture to fit a page resulted in an
axis being scaled by zero. Thanks to Ian Morrison.
[23/06/93] RS !RasMol and RasWin added to the EMBL file server and
anonymous FTP server in Heidelberg, in the directories
/pub/software/dos and /pub/software/unix of
ftp.embl-heidelberg.de
[22/06/93] RS x11win.c
Fixed problem in selecting the required visual class that
caused RasMol to crash when running the OpenWin3 server.
[22/06/93] RS rasmol.h
Added warning messages to the RasMol banner to describe
current visual depth and if not displaying interactively.
[21/06/93] RS molecule.h molecule.c
Added short radius and irad fields to HBond structure
to allow for `thick' hydrogen and disulphide bonds.
[21/06/93] RS pixutils.c command.c render.c outfile.c
Ensured all function prototypes were surrounded by #if
defined(__STDC__) || defined(IBMPC) to avoid errors with
non ANSI C compilers and MS DOS compilers.
[20/06/93] RS Makefile
Added the "-systype bsd43" and "-signed" options to the mips
entry for sysv and bsd43 domains E&S ESV workstations thanks
to Andy Sheppard (mbasd@seqnet.dl.ac.uk)
[18/06/93] RS !RasMol version 2.1 added to the Frequently Asked
Questions (FAQ) list of comp.graphics in the section on
molecular visualization stuff. A RasMol entry ias also
added to the molecular graphics menu of the John Hopkins
University Medical Library Gopher system.
[18/06/93] RS !Announced first public release of RasMol and RasWin
version 2.1, available by anonymous FTP from ftp.dcs.ed.ac.uk
[129.215.160.5] in the directory /pub/rasmol. The announcement
was made in both bionet.software and comp.graphics newsgroups.
rasmol-2.7.6.0/ChangeLog/ChangeLog.2 0000775 0000000 0000000 00000020207 13364034342 0016730 0 ustar 00root root 0000000 0000000 [15/12/93] RS molecule.c
Corrected a bug in the helix determination algorithm that
resulted in helices sometimes being one residue shorter than
Kabsch and Sander's DSSP output. Thanks to Shane Sturrock.
[15/12/93] RS x11win.c
Modified the way that FetchEvent waits for the next XEvent
to allow interactive use on VMS systems and UNIXs without
TERMIOS or select(2) functions.
[14/12/93] RS command.c
Made several changes to ensure that the latest extensions to
RasMol compile on VMS systems without warnings/errors.
[13/12/93] RS x11win.c raswin.c
Ignore mouse movements close to initial starting position.
[13/12/93] RS outfile.c
Corrected bug in "write script" that caused magnifications
such as "zoom 140" to be written as reductions, "zoom 40".
[10/12/93] RS x11win.c
Changed the (default) menu fonts from 12pt to 14pt and fixed
a serious `sprintf' bug, to avoid the program crashing on
machines without the required fonts, such as NCD X-terminals.
Very special thanks to Norm Yamane for the bug fixes.
[10/12/93] RS rasmol.c
Removed the "static" declaration qualifier from HandleEvents
in both the function prototype and main definition to avoid
a feature of the new IRIX compiler that only resolves forward
references in the same file at link time!
[02/12/93] RS tokens.h command.c molecule.c abstree.c abstree.h
Added the predefined set "water"/"waters" that contains
all the heterogenous water molecules; "H0H","WAT" and "H20".
Also allow PDB residue TRY as a synonym for TRY, CPR as a
synonym for PRO and also CSH, CYH and CSM for CYS.
[01/12/93] RS molecule.h
Removed "extern" definitions of [Min,Max][Main,Heta]Atom from
molecule.h that caused the VMS linker to generate unresolved
symbol errors/warnings! Thanks to Carl David.
[29/11/93] RS rasmol.h
Check to prevent redefinition of "PI" if its defined in
, to avoid Linux errors. Thanks to Robert Herzog.
[25/11/93] RS outfile.c
Corrected bug in RasMol "write script" command that caused
some problems of the axes had been rotated by more than 90
degrees (caused by asin). Also fixed RasWin "write script".
[25/11/93] RS command.c
Fixed bug in RasWin that caused molecules to translate and
rotate differently to the UNIX version due to INVERT.
[24/11/93] RS outfile.c outfile.h command.c tokens.h
Prototype implementation of a RasMol "write molscript" command
to generate MolScript script files of the current image. It
currently only outputs the molecule's secondary structure to
generate a ribbon diagram.
[24/11/93] RS molecule.c molecule.h command.c command.h
Modified RasMol to internally keep track of the currently
loaded molecule's original filename.
[23/11/93] RS outfile.c outfile.h command.c
Added the RasMol "write script" command to generate a RasMol
script file containing current parameter values and viewing
transformation.
[23/11/93] RS molecule.c
Convert Alchemy atom names to upper case, and use the file
line number as the atoms serial number to avoid problems.
[23/11/93] RS transfor.c transfor.h command.c
Uncovered RasMol bug that caused RasMol to not execute
rotations in the order they appear in a script file and
applied all X, Y and Z rotations once the file was loaded.
[23/11/93] RS raswin.c
Modify DDEExecuteCommand() to redraw the screen after each
DDE Execute command list. This solves the bug caused by moving
the redraw processing to handle the scroll bars properly.
[22/11/93] RS command.c
Added the RasMol "background" command which is synonymous
with the command "set background" for compatability.
[22/11/93] RS raswin.c
Modified RasWin to only accept mouse movement transformations
only after RasWin detects the preceeding mouse button press.
This avoids spurious translations after using dialog boxes.
[22/11/93] RS command.c
Corrected `logic' problem in RasMol that caused the program to
exit sucessfully if a menu option is selected while loading
a molecule. Menu options are now ignored during loading.
[22/11/93] RS render.c
Corrected bug in IdentifyAtom() that sometimes caused RasMol
to crash when picking "Ball & Stick" representations by not
determining the Chain and Group of the selected bond's atom.
[19/11/93] RS raswin.c
Fixed bug in RefreshScreen handling that only redrew image
if DispatchMessage() was called from the main loop. The screen
is now checked for refresh after each Windows message causing
the molecule to rotate whilst scrolling. Added the UNIX mouse
movement/key combinations to translate/rotate/zoom and slab
the molecule. Picking follows the same rules as RasMol.
[19/11/93] RS mswin31.c
Corrected bug in UpdateScrollBars() moved the button in the
opposite direction to UNIX. Changed TranferImage() to force
the screen to be redrawn immediately.
[18/11/93] RS x11win.c
Added mouse control of rotation, translation, zooming and
slabbing by moving mouse while pressing down a mouse button
and optionally holding either the [shift] or [control] keys.
Picking is by pressing/releasing mouse in the same position.
[17/11/93] RS command.c
Added "reset" command to initialise all the dial values to
their default values. Modified the new filename parsing to
avoid "save xyz.pdb" generating the file ".pdb" and issuing
an error message. File types must be followed by whitespace.
[17/11/93] RS transfor.c
Corrected bug in ColourBackAttrib that resulted in the RasMol
"colour backbone" command colouring everything. Thanks to
Shane Sturrock.
[15/11/93] RS x11win.c
Handle ICCM "WM_DELETE_WINDOW" request from window manager.
Added fatal XIO error handling and `gracefull' shutdown.
[08/11/93] RS command.c
Filenames no longer need to be delimited with either quote
or apostrophe characters in the RasMol load, script, write
and save commands. Filenames beginning with a tilde are now
`globbed' on UNIX systems. Space characters are ignored at
the start of filenames. Try compression file extensions and
environment search paths when loading a file.
[05/11/93] RS command.c transfor.c transfor.h
Permit magnification over 200% based upon the size of the
molecule. Zoom only reports an error if the maximum "image"
size of a sphere (about 120 pixels radius) is exceeded. This
leads to interesting behaviour when enlarging the screen at
maximum magnification ... objects stay the same size!
[05/11/93] RS command.c molecule.c molecule.h
Added the ability to read in compressed file formats.
Currently supported compression formats are UNIX `compress'
(".Z") and GNU gzip (".gz" and ".z") compression formats.
[05/11/93] RS abstree.h
Increased the default VDW radius for unknown atoms to 1.44A.
[01/11/93] RS command.c command.h rasmol.c raswin.c
Disable slabbing and shadows after a RasMol "zap" command.
[01/11/93] RS molecule.c
Remove the use of EndOfData in molecule.c that was creating
problems for the RasMol zap command on certain PDB files.
[22/10/93] RS molecule.c
Modified FetchRecord to use either line feed '\n' or carriage
return '\r' as line terminator to support Mac format files.
[22/10/93] RS rasmol.c
Placed HandleEvents function prototype inside #ifdef __STD__
after changing it to take a paramter. Thanks to Joseph Warden.
[20/10/93] RS rasmol.c
Include instead of , to allow the
program to be compiled under 386BSD. Thanks to Robert Miller.
[17/10/93] RS rasmol.c
Include if _AIX is defined for IBM RS/6000s
under AIX 3.2. Thanks to John Harvey.
[15/10/93] RS rasmol.c
Added #include to rasmol.c, when _SEQUENT_ is
defined to allow struct fd_set to be properly defined.
[15/10/93] RS rasmol.c
Solved problem that LexState is not defined when TERMIOS is
undefined, and never initialised. Thanks to John Harvey.
[15/10/93] RS !Announced the public release of RasMol and RasWin
versio 2.2, available by anonymous FTP from ftp.dcs.ed.ac.uk
[129.215.160.5] in the directory /pub/rasmol. The announcement
was made in both bionet.software, bionet.announce, sci.bio,
sci.chem, comp.graphics.visualisation newsgroups.
[13/10/93] RS !RasMol/RasWin version 2.2 presentation given at
Glaxo Group Research, Greenford, Middlesex.
rasmol-2.7.6.0/ChangeLog/ChangeLog.3 0000775 0000000 0000000 00000007352 13364034342 0016737 0 ustar 00root root 0000000 0000000 [02/03/94] RS pixutils.c
Improved the efficiency of the RasMol polygon rendering.
[02/03/94] RS command.c tokens.h
Added the "colour trace" command (and the "trace" command)
to make "trace" synonymous with the "backbone" command.
[01/03/94] RS abstree.c abstree.h command.c tokens.h
Added the rasmol "define" command to allow sets to be
defined by the user.
[01/03/94] RS command.c tokens.h
Added the RasMol "echo" command.
[28/02/94] RS outfile.c
Improved the implementation of "write vectps" to correctly
handle wireframe intersections with spheres and to draw
cylinder bonds to produce effective ball & stick pictures.
[22/02/94] RS command.c render.c transfor.c
Added nucleic acid ribbon representations. By default, a
nucleic acid ribbon is 720 RasMol units wide. The O5* atom
defines the RNA ribbon plane, and the midpoint between O5*
and O2P defines the DNA ribbon plane.
[21/02/94] RS command.c tokens.h render.h
Added RasMol commands "set axes", "set boundbox" and "set
unitcell" to display additional objects.
[17/02/94] RS transfor.c transfor.h
Added the RasMol command "colour structure" to colour proteins
by secondary structure type. Removed the "user" colour option
from the UNIX menu system and replaced with "structure".
[16/02/94] RS command.c transfor.c
Changed the semantics of "ribbons 0" and the RasMol "ribbons"
menu option to display ribbons whose width varies by secondary
structure type.
[15/02/94] RS rasmol.c raswin.rc
Changed the menu item "Save" to "Export" which makes more
sense for generating image files.
[14/02/94] RS raswin.c x11win.c graphics.h command.c tokens.h
Added the "set mouse" command to RasMol to allow the RasMol
mouse bindings to emulate other packages. RasMol currently
supports "set mouse insight" and "set mouse quanta".
[13/02/94] RS rasmol.1 rasmol.hlp rasmol.html raswin.hlp
Completed work on the RasMol "on-line" help preparation
system. Now the UNIX man pages, Microsoft Windows help,
Mosaic HTML and RasMol/RasWin online help is prepared from
the same source. All these files are now up to date.
[10/02/94] RS command.c tokens.h molecule.c molecule.h
Added the rasmol "show symmetry" command.
[27/01/94] RS rasmol.c
Improved command line editting under VAX VMS. Fixed VMS bug
that caused the process to "crash" after RasMolExit().
[26/01/94] RS rasmol.c
Extended VAX VMS port of RasMol using ASTs to allow the
asynchronous receipt of characters from SYS$INPUT:
[26/01/94] RS graphics.h command.c
Allow the command line state (prompt) to enable/disable
the menu buttons, this solves a GUI style flaw/bug.
[07/01/94] RS molecule.c transfor.c
Corrected potential bugs when detailing with upper and lower
bounds on Main and Heta residue numbers and temperatures.
[07/01/94] RS x11win.c
Made the second and third mouse buttons synonymous.
[07/01/94] RS molecule.c molecule.h command.c tokens.h
Added the RasMol "renumber" command to ensure sequential
residue numbering alongs macromolecular chains.
[07/01/94] RS transfor.c transfor.h command.c tokens.h
Added the RasMol "centre" command to allow rotation of a
molecule about the centre of gravity of a given set of atoms.
[06/01/94] RS x11win.c
Solved colourmap problem on Silicon Graphics machines that
caused some colours to be displayed incorrectly!
[06/01/94] RS abstree.c
Corrected bug in ParsePrimitiveExpression that caused general
wildcards (i.e. "*" and "*.*") to be treated incorrectly.
[05/01/94] RS x11win.c
Renamed the variable "shminfo" to avoid a name clash when
compiling on the DEC Alpha using OSF/1 and Ultrix. Thanks
to Dan Jacobson.
[04/01/94] RS !Started visiting research post with the
Protein Biochemistry group at Glaxo Group Research,
Greenford, Middlesex.
rasmol-2.7.6.0/ChangeLog/ChangeLog.4 0000775 0000000 0000000 00000025621 13364034342 0016737 0 ustar 00root root 0000000 0000000 [06/06/94] RS raswin.c rasmol.h molecule.c render.c
Completed port of RasMol v2.4 to Windows NT. Thanks to
David Stranz and David Digby.
[05/06/94] RS outfile.c
Corrected bug in generating Vector Postscript in RasWin,
resulting in the image appearing inverted on the page.
Thanks to Tomasz Heyduk.
[01/06/94] RS raswin.c raswin.rc raswin.idm
Added CHARMm format files to the RasWin file open dialog box
and added the "Strands" menu item to the "Display" menu.
[01/06/94] RS outfile.c transfor.c transfor.h
Optimised representation of molecule in generated RasMol
script files by detecting "cpk" colours and VdW radius.
[31/05/94] RS outfile.c
Added complete support for writing out the current molecule
representation in a RasMol script file using "write script".
[31/05/94] RS molecule.c transfor.c
Improved lazy calculation of hydrogen bonding and disulphide
bridges, hence "hbonds off" and "colour hbonds none" no longer
force evaluation.
[27/05/94] RS command.c render.c transfor.c
Modified the DisplayRibbon routine to allow the simultaneous
display of strands and ribbons. Removed the "set ribbons"
command and replaced it with "ribbons" and "strands".
[26/05/94] RS transfor.c render.c
Changed the way that ribbons are selected and rendered in
different colours. This brings the ribbon rendering in line
with alpha carbon position and colouring.
[23/05/94] RS molecule.c
Corrected bug in LoadAlchemyMolecule that resulted in molecules
having the wrong chirality. Thanks to Mikhail Matrosovich.
[20/05/94] RS outfile.c
Improved the Molscript script file interface. The RasMol
"write molscript" command now stores the scaling, translation
and slabbing (z-clipping) information. Thanks to Kevin Gardner.
[20/05/94] RS raswin.c
Corrected bug that caused the DIB copied to the clipboard or
DDE'ed to another application to have the wrong colour map.
[19/05/94] RS molecule.c
Corrected bug in RasMol that caused it to report far too many
ladders in DSSP. Changed references to "Ladders" to "Strands".
[19/05/94] RS molecule.c molecule.h command.c tokens.h
Added support for CHARMm format co-ordinate files. Thanks to
Charles Brooks.
[18/05/94] RS molecule.c
Removed interchain bonding. This makes loading a multi-chain
protein faster and allows for RMS fitting with RasMol.
[18/05/94] RS command.c tokens.h transfor.c transfor.h render.c
pixutils.c
Added a second colour to RasMol strands ribbons. Hence, the
command "colour ribbons1 blue" and "colour ribbons2 red"
draws blue ribbons with the outmost stands in red.
[17/05/94] RS command.c render.c render.h
Renamed the command "set dots" to "set radius" and added the
command "set solvent" which controls the dot surface as
either VDW or solvent accessible. The radius controls either
the VDW radius or the Solvent Probe Sphere radius.
[16/05/94] RS raswin.c
Added scroll bar and terminal history to the RasMol command
line window. Improved scrolling in resized windows.
[12/05/94] RS raswin.c rasmol.c mswin31.c transfor.c
Corrected bug in RasMol that resulted in the "specular",
"specpower" and "ambient" parameters not being reset by a
RasMol "zap" command and fixed initial RasWin CMap.
[12/05/94] RS command.c tokens.h abstree.c abstree.h
Added the atom property "elemno" that uniquely identifies
each atoms element type, hence "select elemno=26" identifies
all sulphur atoms.
[12/05/94] RS molecule.c
Added a test to check if the PDB x, y and z co-ordinates of
an atom are 9999.000 indicating an XPLOR pseudo atom. Thanks
to Chris Littler and Harren Jhoti.
[11/05/94] RS command.c render.c render.h
Added the command "set dots " to set the probe
sphere radius for calculating the solvent accessible
surface of a protein.
[11/05/94] RS render.c
Corrected bug when drawing thin cylinders since the change
to DrawTwinLine for axes, bounding box and unit cell.
[10/05/94] RS raswin.c
Corrected bug in the DDE formating of the picked atoms
co-ordinates.
[10/05/94] RS molecule.c
Fixed bug in RasMol that incorrectly determined the lowest
residue number in PDB files that are unordered. Thanks to
Ken Davis.
[09/05/94] RS molecule.c molecule.h command.c render.c tokens.h
Fully implemented the RasMol commands "set unitcell" and
"show symmetry", these now take the crystal symmetry
information from the CRYST1 record of a PDB file.
[03/05/94] RS render.c
Corrected RasWin problem in DisplayRibbon caused by rounding
when interpolating Z-coordinates with large ZOffset.
[03/05/94] RS transfor.c
Corrected RasWin overflow bug in ScaleColourAttrib that
caused `hot' atoms to be displayed black instead of red.
[03/05/94] RS rasmol.doc
Corrected several typographic mistakes and errors within
the rasmol documentation. Thanks to Naoum Salame.
[29/04/94] RS raswin.c mswin31.c
Managed to trace a RasWin colour map initialisation problem
that occasionally caused RasWin to crash with a GDI error or
start with wrong colour background. Thanks to Dave Digby.
[28/04/94] RS x11win.c
Corrected buffer char types in x11win.c that were causing
warnings on pedantic compilers. Thanks to Ethan Merritt.
[20/04/94] RS outfile.c
Added support for vector PostScript output of dot surfaces.
[20/04/94] RS render.c render.h command.c transfor.c transfor.h
tokens.h
Added a Van der Waals dot surface representation to RasMol.
The command "dots " enables and disables a dot
surface of the currently selected atoms. "dots " can
control the dot density, "colour dots" colours the whole
dot surface a given colour [the default is taken from atoms]
[20/04/94] RS rasmol.c
Corrected bug with including on Evans & Sutherland
ESV workstations.
[19/04/94] RS render.c
Solved a bug in IdentifyAtom that refused to identify picked
non-connected atoms when bonds are being displayed.
[19/04/94] RS molecule.c
Corrected bug in loading alchemy format files. Atom serial
numbers were incorrect resulting in incorrect bonding. Thanks
to Ben Gaskins.
[18/04/94] RS render.c render.h tokens.h command.c
Added the commands "set axes" and "set boundingbox" to display
the co-ordinate axes and molecule bounding box on screen.
[18/04/94] RS pixutils.c
Corrected bug in routines `ClipLine' and `ClipVector' which
caused lines that clipped the bottom of the screen to bend.
[18/04/94] RS raswin.c
Corrected bug in the DDE transfer of CF_DIB objects for the
DDE "Image" item. Thanks to Dave Digby and Ken Davis.
[15/04/94] RS rasmol.c raswin.c abstree.h transfor.c molecule.c
molecule.h
Better support for the display of small molecules. Smaller
bond cylinder radius for `sticks' images of molecules with
less than 256 atoms, and use unadjusted Van der Waals radius
for molecules containing explicit hydrogen atoms.
[15/04/94] RS molecule.c
RasMol now uses the connectivity specified in PDB CONECT
records when displaying molecules with less than 256 atoms,
i.e. small compounds. Thanks to Brian Dunford-Shore.
[14/04/94] RS rasmol.h raswin.c
Extended the range of items exported by DDE to include the
picked atom's co-ordinates and the image being drawn on
the screen (transfered as CF_DIB).
[13/04/94] RS raswin.c
Improved the processing of WM_SIZE handling by increasing
XRange to be long aligned rather than decreasing it. This
avoids the occasional black line down the side of the screen.
[13/04/94] RS transfor.c
Corrected bug in transfor.c that cleared more entries in
in the StructShade table than there were. This sometimes
caused RasMol to crash later during keyword lookup.
[12/04/94] RS rasmol.c
Changed the TERMIOS handling section to support FreeBSD1.1
using XFree2.x. Special thanks to Pedro A M Vazquez.
[11/04/94] RS molecule.c
Corrected bug in RasMol that caused residues with different
insertion codes to be placed in the same group. They're now
placed in consecutive Groups but with the same serial number
hence may be "renumbered". Thanks to Anne Cleasby.
[07/04/94] RS molecule.c
Corrected bug in sizing molecule read from an MDL Mol file.
[05/04/94] RS molecule.c molecule.h command.c tokens.h raswin.c
rasmol.c
Added support for reading in files in Molecular Design Ltd's
(MDL) Mol file format.
[30/03/94] RS rasmol.doc
Corrected HTML bug that caused the NCSA PC Mosiaic viewer to
crash when displaying rasmol.html.
[28/03/94] RS pixutils.c
Corrected a bug in RenderPolygon that caused a floating point
division by zero error and huge/far segment problems on the
IBM PC.
[25/03/94] RS outfile.c
Finished implementing correctly intersecting spheres when
outputing vector postscript. However, this may cause
problems for low memory laser printers.
[23/03/94] RS transfor.c
Corrected bug that set the default scale too large for very
small molecules.
[22/03/94] RS molecule.c
Handle incompletely specificed @MOLECULE records in
Sybyl Mol2 files such as those exported from InSight. Handle
`small molecule' atom names (containing serial numbers) in
PDB files. Thanks to Martin Hargreaves
[18/03/94] RS pixutils.c
Improved the polygon rendering algorithm. RasMol now displays
solid ribbons as gouraud rather than constant normal shaded
polygons.
[18/03/94] RS rasmol.c
Added the command line options "-pdb", "-alchemy", "-mol2"
and "-xyz" to specify the format of the file given on the
command line.
[17/03/94] RS molecule.h command.h
Increased the maximum filename length from 80 to 256 chars.
[15/03/94] RS outfile.c outfile.c command.c
Improved the quality of "vectps" output. RasMol now correctly
handles intersection of spheres in vector PostScript output.
The use of `cartoon' outlines is now controlled by the
"set vectps " command.
[14/03/94] RS x11win.c
Change Visual detection code for 24bit and 32bit displays to
support both TrueColor and DirectColor. This adds support for
the HP 735 CRX-24. Special Thanks to Thomas Lew.
[11/03/94] RS outfile.c
Improved speed of vector PostScript printing by performing
sphere and bond culling before sorting/generating output.
[11/03/94] RS molecule.c molecule.h command.c tokens.h raswin.c
Added support for MSC XMOL's XYZ format files.
[10/03/94] RS molecule.c molecule.h command.c tokens.h raswin.c
Added support for Sybyl .mol2 file format for reading in
a file (i.e. "load mol2"). Read small molecule connectivity
from "alchemy" and "mol2" files, if it exists.
[09/03/94] RS x11win.c
Allow the EIGHTBIT version of RasMol to display on 8-bit
grey-scale X displays. Special thanks to Gerald Loeffler.
[09/03/94] RS molecule.c
Allow backbone traces to be drawn to unknown residues
that contain an alpha carbon.
[04/03/94] RS !Announced the public release of RasMol and
RasWin version 2.3, available by anonymous FTP from
ftp.dcs.ed.ac.uk [129.215.160.5] in the directory
/pub/rasmol. The announcement was made in both
bionet.software, bionet.announce, sci.bio,
sci.chem, comp.graphics.visualisation newsgroups.
rasmol-2.7.6.0/ChangeLog/ChangeLog.5 0000775 0000000 0000000 00000026071 13364034342 0016740 0 ustar 00root root 0000000 0000000 [25/10/94] RS molecule.c molecule.h command.c abstree.h
Once again improved the method rasmol uses to determine
bonding by maintaining the covalent radius of every element.
The "connect " command has been implemented.
[24/10/94] RS rasmac.c molecule.c outfile.c script.c
Associated a file creator, a file type and an icon with all
of RasMac's output files; clicking on kinemage output starts
Mage. Fixed compatability problem with metrowerks C compiler.
[24/10/94] RS raswin.c mswin31.c command.c transfor.c render.c
outfile.c
Made several changes to RasMol to allow it to compile under
Microsoft Windows. Added command line options to raswin.
[24/10/94] RS rasmac.c rasmac.rsrc
Added the ability to detect a file's type information when
using apple events. Also added handing of 'mMOL' signature
used by MDL's MOL files. This allows Mol files and RasMol
scripts to be treated sensibly when dragged & dropped.
[20/11/94] RS x11win.c
Added an XQueryExtension test to OpenDials to avoid problems
on servers that don't understand XInputExtension. Changed
MITSHM to use XQueryExtension rather than the undocumented
XShmQueryExtension call. Fixed MacX popup menu problem.
[20/11/94] RS transfor.c transfor.h command.c tokens.h
Implemented the RasMol "colour dots potential command".
[19/10/94] RS rasmac.c rasmac.rsrc
Implemented File Open, Save and Export Dialog boxes.
[18/10/94] RS x11win.c rasmol.c graphics.h command.c
Finished completely rewritting the X User Interface to comply
with the OSF Motif guidelines.
[14/10/94] RS abstree.c
Added the american spellings of the elements ot RasMols'
exception table; cesium, aluminum and sulfur.
[13/10/94] RS applemac.c rasmac.c
Implemented RasMac's About and Fatal Error Message Dialog
boxes. Also implemented "paste" into the terminal window.
[12/10/94] RS x11win.c
Fixed a bug in RasMol caused by displaying a 32bit image
on a machine with the opposite byte order, e.g. AXP & SGI.
[12/10/94] RS applemac.c
Fixed bug in ClipboardImage and improved printer handling.
[11/10/94] RS rasmac.c applemac.c rasmac.rsrc
RasMac now interprets the `core' Apple Events and `works'
under MacMosaic. At present assumes all files are PDB data.
Implemeted "Print", "Copy" and "Page SetUp" menu options.
Fixed some portability problems for Metrowerks C.
[10/10/94] RS outfile.c
Implemented generation of 32bit PICT files.
[07/10/94] RS outfile.c outfile.h command.c tokens.h
Added the ability to generate PICT images on all platforms
when running the 8bit version of RasMol.
[07/10/94] RS command.c command.h
Avoided problems zooming when no molecule is loaded. Made
TokenValue a Long, this corrects bug in over zooming.
Forced function prototypes on Macs as well as ansi C & PCs
[07/10/94] RS x11win.c
Provided (compromise) better support for 32/24bit X displays
that are not RasMol endian, this displays images correctly
on the screen but generates incorrect raster files!
[06/10/94] RS script.c command.c command.h
Added file format to the load statement and added UNIX style
scripting comment to the generated RasMol scripts.
[06/10/94] RS command.c command.h
Fixed bug in RasMac that caused file names to be converted
to upper case and truncated at the first space [like RasWin].
[06/10/94] RS Imakefile rasmol.h command.c rasmol.c
Improved the RasMol Imakefile. Added much better support
for HP-UX version 9.x. Special thanks to Richard Lloyd.
[06/10/94] RS render.h
Fixed Ribbons bug caused by isqrt on sun386i machines!
[28/09/94] RS applemac.c
Implemented dither mode CopyBits transfers when displaying
on screens with less than 256 colours.
[26/09/94] RS rasmac.c applemac.c
Reorganised mouse movement processing using null events similar
to the Windows version. Implemented all 'MouseMode's using the
option and command keys. Added 'Edit' Menu to main Menu.
[26/09/94] RS molecule.c
Treat 'END' records identically to 'TER' records, allowing PDB
files to be concatenated.
[23/09/94] RS rasmol.h
Fixed a problem with the "ToUpper" macro on the Evans and
Sutherland ESV caused by non-ansi C compiler (like sun386i).
[23/09/94] RS molecule.c
Made several changes to the processing of PDB files. TER
now forces a split between chains (with identical chain idents)
Protein mainchain hydrogen bonding only within a single chain.
[23/09/94] RS x11win.c
Extended RasMol's handling of dials boxes to allow the use of
Silicon Graphics' "Absolute" mode dials box. This fixes several
usability problems. Thanks to Steve Jordan.
[22/09/94] RS abstree.c
Made '#' synonymous to the wildcard '?' in atom names.
[22/09/94] RS script.c
No longer comment out the load command in scripts generated
by the "write script" command. Thanks to Paul Charifson.
[16/09/94] RS tokens.h transfor.h transfor.c command.c
Introduced the colour scheme "charge". This is identical
to temperature except high values are blue, low are red.
[16/09/94] RS graphics.h applemac.c transfor.c
Corrected bug in 32bit RasMol when using more than 256
colours, e.g. "colour group". Implemented 32bit Mac version.
[15/09/94] RS x11win.c
Finally corrected problem with colour map flashing on SGI
Personal Iris Machines caused by Enter & Leave Notification.
Deleted unused functions "AllocSharedMem" and "FreeSharedMem".
[15/09/94] RS rasmac.c applemac.c render.c command.c command.h
Ported RasMol to compile on both the Apple Machintosh
and the PowerPC (native) using the Metrowerks C compiler.
[15/09/94] RS abstree.h abstree.c
Revised the Van der Waals radii for all the elements in
the periodic table. Atomic symbol 'Lw' is same as 'Lr'.
[14/09/94] RS command.c
Added the function FetchFloat to allow the user to specify
real (fixed point) values. All commands taking distances in
RasMol units (including "set radius" and "within") may now
also specify real values in Angstroms. "Slab", "zoom",
"rotate" and "translate" may also take non-integral values.
[14/09/94] RS molecule.c
Extended RasMol's handling of CONECT records using the
'pseudo-convention' that double and triple bonds are
specified twice and three times respectively. Thanks to
Jeff Blaney and Dave Weinenger.
[14/09/94] RS command.c
Improved the syntax of RasMol atom expressions. It is now
possible to specify a chain after a residue number or range
of residue numbers, e.g. select 5-8:a, 4b, 1:1, 6:*
[14/09/94] RS script.c script.h
Modified the algorithm used for outputing bonds (including
backbone, hbonds and ssbonds) in WriteRasMolScript. This
significantly reduces size of some resulting script files.
Also corrected a bug outputing scripts containing ribbons.
[11/09/94] RS rasmac.c applemac.c RasMac.rsrc
Completed initial port of RasMol to the Apple Machintosh.
All that remains to be done are the apple specific dialog
boxes and apple events.
[01/09/94] RS command.c
Corrected a bug in LoadFile that caused the file depth to
be reset. This resulted in `DisplaySelectCount' showing
the result of each operation in a RasMol script.
[01/09/94] RS script.c script.h outfile.c outfile.h
Split the RasMol module "outfile", to produce a new module
"script" responsible for generating script like output
files. This avoids the 32K per segment limit on the Apple
Machintosh.
[09/08/94] RS transfor.c
Corrected bug in CPKColourAttrib that assumed there were
only seven CPK colours. This caused compounds containing
heavy atoms to be displayed in the wrong colour.
[09/08/94] RS pixutils.c
Corrected two bugs that were producing incorrectly drawn
vectors. The first in ClipVector resulted in lines never
being partially clipped, the other a bug in DrawTwinVector.
[08/08/94] RS outfile.c
Improved quality of MolScript and Kinemage output files.
[04/08/94] RS transfor.c transfor.h render.c
Improved implementation of shadowing using the fact that
the inverse of a general rotation matrix is its transpose.
This should improve the RasMol critical path!
[02/08/94] RS molecule.c
Implemented the function ReadPDBCoord to allow RasMol to
read in Chem3D format PDB files. Thanks to Henry Rzepa.
[02/08/94] RS command.c
Disabled the use of "save" and "write" commands in RasMol
scripts. This avoids security problems when used with the
internet. Thanks to Martin Hargreaves and Ian Dunkin.
[01/08/94] RS Makefile
Fixed problem that resulted in getpwnam only searching the
local /etc/passwd and not NIS. Thanks to Mike Hann.
[27/07/94] RS abstree.h abstree.c command.c
Added element name to periodic table to allow the use
of element names, and their corresponding plurals, as
predefined set names containg all elements of that type.
For example, "select chlorines" and "select zinc".
[22/07/94] RS raswin.c
Implemented "Drag & Drop" functionality in RasWin.
[20/07/94] RS font.h pixutils.c pixutils.h render.c command.c tokens.h
Implemented prototype atom labelling in RasMol. The commands
"label ", "colour label " and "set fontsize
" are all implemented. Needs more work on label
placement, clipping and optimisations.
[14/07/94] RS rasmol.c
Extended cursor key mappings in to handle DEC and ANSI control
sequences for cursor keys in application mode.
[14/07/94] RS abstree.c abstree.h transfor.c transfor.h render.c molecule.c
Completed support for entire periodic table of elements. This
now uses a single structure for VdW radius and CPK colours.
The property "elemno" now specifies the atom's atomic number.
[11/07/94] RS tokens.h command.c
Made the keyword 'source' synonymous with 'script', and
the keyword 'mainchain' synonymous with the predefined
set backbone.
[08/07/94] RS tokens.h command.c molecule.c
Introduced the command 'connect' to force RasMol to
determine the bonding of the current molecule.
[29/06/94] RS molecule.c
Corrected bug in LoadPDBMolecule that resulted in CONECT
records from Pat Walter's "babel" being misinterpreted.
[24/06/94] RS outfile.c
Improved the quality of stick bonds in Vector PostScript by
shading them by their angle to the viewer.
[23/06/94] RS outfile.c rasmol.doc
Corrected problem in WriteScriptFile that resulted in
syntax errrors in RasMol script files describing hydrogen
(and disuplhide) bonding patterns. Thanks to Martti Tolvanen.
[17/06/94] RS command.c
Introduced the file format "RasMol" to the write command
which is equivalent to the "Script" format specifier.
[14/06/94] RS raswin.c
Corrected minor bug that caused the About dialog box in
Windows NT not to display the processor type. Special
thanks to Pedro Mendes.
[13/06/94] RS rasmol.doc manual.doc manual.ps
Corrected Dreiding spelling mistake in rasmol.doc and fixed
problem with manual.ps caused by a bug in the PostScript
printer driver supplied by Microsoft.
[09/06/94] RS !Announced the public release of RasMol and RasWin
version 2.4, available by anonymous FTP from ftp.dcs.ed.ac.uk
[129.215.160.5] in the directory /pub/rasmol. The announcement
was made in bionet.software, bionet.announce, sci.bio,
sci.chem, comp.graphics.visualisation, bionet.xtallography
and sci.techniques.xtallography newsgroups.
rasmol-2.7.6.0/ChangeLog/ChangeLog.6 0000775 0000000 0000000 00000026227 13364034342 0016744 0 ustar 00root root 0000000 0000000 [05/05/95] RS render.c
Corrected 16bit precision problem with cartoons on PCs and
Macintoshes. These caused rounding errors in `ribbons'.
[02/05/95] RS INSTALL
Added additional build info for RasMac on the PowerPC using
Metrowerks C++ v1.2. This requires additional files to v1.1.
Special thanks to Graham Palmer.
[03/04/95] RS pixutils.c pixutils.h render.c command.c
Added the ability to display dashed "strands" ribbons.
[03/04/95] RS render.c
Modified the handling of the first and last residue in
a chain to only extend to the alpha carbon except when
the last residue is an arrow head.
[27/03/95] RS render.c
Fixed bug in cartoon representation when final residue in a
chain is a beta-sheet. Improved "CalculateInten" performance.
[27/03/95] RS rasmol.c
Made several changes to rasmol.c to allow RasMol to compile
with DEC C (on AXP and VAX) without /standard=vaxc. Special
thanks to Martin Zinser.
[26/03/95] RS render.c render.h pixutils.c pixutils.h command.c
tokens.h
Added the new representation "cartoon" which represents a
protein as a Richardson-style cartoon. The width of the
cartoon is given as a parameter, the depth of the ribbon
and use of arrow heads may be changed using "set cartoon".
[25/03/95] RS render.c command.c transfor.c molecule.h
Changed the semantics of the "trace" command and added a
new representation, "trace" which displays a cylindrical
spline representation of "backbone".
[22/03/95] RS render.c render.h command.c tokens.h transfor.c
script.c
Added the "Monitor" representation to RasMol as an dashed
line between two atoms, optionally labelled by the distance
between the atoms (the default).
[16/03/95] Makefile
Added comments about use of +O4 optimisation using HPUX 9.05
on the native PA-RISC compiler. Thanks to Richard Mathar.
[13/03/95] RS outfile.c
Implemented dashed lines in RasMol's vector PostScript output.
This now includes the ability output of hbonds and ssbonds.
[13/03/95] RS script.c
Fixed bug when generating RasMol scripts caused by overlapping
datum type masks. This caused errors with dashed vectors.
[12/03/95] RS x11win.c
Fixed a problem using scroll bar arrows to spin a molecule
with three-button emulation on XFree (Linux and NetBSD).
[07/03/95] RS render.c
Improved performance of "isqrt" routine, the most frequently
called function when rendering ribbons.
[06/03/95] RS render.c
Implemented the routine "InitialiseTables" to avoid using
"isqrt". This drastically reduces the start-up time.
[06/03/95] RS render.c
Improved rendering of double & triple bonds.
[03/03/95] RS command.c render.c render.h pixutils.c
Added the ability to display double and triple bonds as
two and three lines using the "set bonds true" command.
[03/03/95] RS command.c tokens.h render.c transfor.c script.c
rasmol.c
Added the ability to display bonds and backbones as dashed
lines using either the "dashes" command or the "dashes"
parameter to the "wireframe" and "backbone" commands.
[03/03/95] RS command.c
Modified 'FetchFile' to display explicitly specified
hydrogen bonds by default.
[03/03/95] RS pixutils.c
Improved quality of dashed lines.
[02/03/95] RS render.c molecule.c transfor.c transfor.h
Ported RasMol to compile under Borland's Turbo C/C++. This
required rewrite of ClearBuffers to avoid "_fmemset" bug.
[02/03/95] RS outfile.c outfile.h command.c tokens.h x11win.c
rasmol.c
Added support for Silicon Graphics' IRIS RGB format image
files for both 8 and 32bit versions, "write iris ".
[01/03/95] RS outfile.c
Tidied up many of the image file output routines.
[28/02/95] RS molecule.h abstree.c abstree.h
Improved handling of RNA bases and conversion of non-standard
nucleotide atom names. Thanks to Hans Hoppe.
[17/02/95] RS molecule.c
Finally implemented internal to cartesian co-ordinate
conversion for MOPAC internal input files. Very special
thanks to Klaus-Peter Gulden.
[16/02/95] RS molecule.c
Added detection of MOPAC file types, and added support
for MOPAC cartesian co-ordinate input files.
[15/02/95] RS molecule.c
Added support for reading MOPAC output files including
charge information (provided the job doesn't use the
"NOXYZ" keyword as an option).
[14/02/95] RS render.c
Added "X", "Y" and "Z" axes labels to the "set axes on"
command.
[13/02/95] RS render.c render.h command.c
Implemented the "set picking centre" command to allow the
centre of rotation to be selected by clicking on an atom.
[10/02/95] RS render.c render.h pixutils.c pixutils.h command.c tokens.h
Started adding more support for RasMol stereo viewing.
Stereo is enabled by either "stereo on" or "set stereo on".
[10/02/95] RS pixutils.c
Improved performance of function DisplayString avoiding
clipping and reduced intensity of atom labels.
[09/02/95] RS abstree.c
Implemented function 'CalcTorsion' for "set picking torsion".
[06/02/95] RS render.c
Increased the maximum sphere rendering radius within RasMol.
This is the first step to producing high-resolution output.
[02/02/95] RS abstree.c abstree.h command.c tokens.h
Added support for selecting individual models in "nmrpdb"
files, either use "model=25" property or expression "::25".
RasMol also now allows chains to be specified ":a" and ":1".
[01/02/95] RS outfile.c
Modified the vector Postscript output routines to saturate
sphere colouring following "set ambient 100".
[23/01/95] RS abstree.c
Added the "%m" label format specifier for amino acid codes.
[20/01/95] RS render.c render.h rasmol.c x11win.c
Added the menu option "Labels" to RasMol for easy labelling.
Improved internal label handling.
[20/01/95] RS abstree.c
Made functions CalcAngle and CalcDistance more robust.
[18/01/95] RS transfor.c transfor.h command.c command.h
Modified the RasMol "restrict" command to disable the display
of backbone, ribbons and strand representations. Labels??
[18/01/95] RS script.c
Corrected bug in Kinemage format output that occurred when
bonds were displayed in some chains but not in others. Also
fixed potential problems with backbone DNA hydrogen bonds
in Kinemage files. Thanks to Piotr Zimniak.
[18/01/95] RS command.c render.c x11win.c rasmac.c raswin.c abstree.
Added the options "distance", "angle" and "torsion" to
the RasMol "set picking" command to inspect geometry.
[17/01/95] RS command.c tokens.h render.c render.h
Added the RasMol command "set picking" with options "none",
"ident" (default) and "label". The final option toggles the
display of atom labels on the picked atom.
[13/01/95] RS command.c
Added the "set write" command to allow "write" and "save"
commands to work from the command line.
[13/01/95] RS command.c tokens.h x11win.c
Added "refresh" command to update screen from script file.
[12/01/95] RS render.c
Modified DrawRibbon to use divisons rather than right shifts.
This corrects problems on Convex. Thanks to Andy Quick.
[06/01/95] RS molecule.h molecule.c abstree.c render.c transfor.c
Modified the "Atom" structure definition to contain atomic
number, this allowed correct determination of Brookhaven
NAD and CoenzymeA elements by changing GetElemNumber().
[16/12/94] RS raswin.c raswin.rc raswin.idm rasmac.c
Modified the menu ogranisation of RasWin to include an Edit
menu containing "Select All" and a "Print SetUp..." option.
[16/12/94] RS molecule.c
Corrected bug reading CHARMm format files that sometimes
placed different residues in separate chains. Thanks to
Stefan Fischer.
[15/12/94] RS script.c
Fixed bug in WriteMolScriptFile that occasionally resulted
in all residues additionally being displayed as coil.
[13/12/94] RS molecule.c molecule.h command.c rasmol.c raswin.c
Added the "nmrpdb" file format to allow all NMR conformations
to be loaded into RasMol into different `models'.
[08/12/94] RS command.c
Corrected a bug in command.c that resulted in an error if
a label string wasn't placed between string terminators.
[08/12/94] RS rasmol.c
Corrected bug in RasMol performance profiling routines.
[08/12/94] RS x11win.c
Improved support for monochrome X. The improved performance
algorithm now performs bidirectional error diffusion and
correctly handles Black/White bit variations (e.g NEC & SUN).
[30/11/94] RS molecule.c
Modified LoadAlchemyMolecule and ConnectAtoms to enable
hydrogen bonding to be specified in Alchemy format files.
Fixed bug with bond types. Thanks to Chris Wilson.
[30/11/94] RS outfile.c
Changed the creator and file type of PostScript files on
the Mac to 'vgrd' and 'TEXT' respectively. This enables
printing by Apple's PostScript utility. Thanks to Tom Jovin.
[29/11/94] RS x11win.c
Added support for Monochrome only X Windows displays by
dithering 8bit images before calling XPutImage. The current
error term diffusion algorithm may have to be improved for
wireframes and dot surfaces. Thanks to Cheuk-san Edward Wang.
[28/11/94] RS molecule.c
Made several changes to RasMol to account for unconventional
atom naming in PDB files, such as strange hydrogens 'HD',
'HG' and 'HH' and cysteine sulphurs ' SB1'. Thanks to Bruce
Livett.
[28/11/94] RS rasmol.doc
Added "primitives" to the keyword list in the on-line help
documentation to solve xref `bug'. Thanks to Steve Brenner.
[21/11/94] RS molecule.c
Changed the handling of PDB residue synonyms to make name
comparison more efficient. Added synonyms for standard
nucleic acids. Thanks to Hans Hoppe.
[21/11/94] RS rasmol.c
Corrected problem with the static forward declaration
of HandleEvents that caused problems on IRIX 4.0 compilers.
Thanks to Noham Weinberg.
[16/11/94] RS rasmol.c command.c
Implemented the "Save As..." option on the File Menu in
the UNIX version of RasMol. Thanks to Henry Rzepa.
[11/11/94] RS molecule.c
Added the ability to read in connectivity records from
columns 32 and 37 of PDB's CONECT records. These are used
by some programs for heavy elements instead of hbonds!
[10/11/94] RS abstree.h
Corrected errors in the covalent radii of several of the
heavy elements in the periodic table.
[08/11/94] RS molecule.c
Corrected a bug in FindSybylResNo that resulted in the wrong
atom types being found in Mol2 files. Thanks to Jim Bentley.
[08/11/94] RS rasmol.h outfile.c
Corrected problem with undefined _fstricmp in raswin.c and
funtion WriteIRISFile under Windows NT. Thanks to Pedro Mendes.
[08/11/94] RS descrip.mms
Corrected several typos. Thanks to Ulrich Schmitt.
[08/11/94] RS render.c script.c
Fixed bug in RasMol that resulted in a division by zero
when "set unitcell on", but the PDB file contains no
crystal unit cell information. Thanks to Arne Eofsson.
[01/11/94] RS pixutils.c
Corrected bug in routines SolidRibbon and StrandRibbon
that didn't specify __far pointers to Knots despite the
defintion in pixutils.h. Announced RasWin version 2.5.1!
[28/10/94] RS !Announced the public release of RasMol, RasMac
and RasWin version 2.5, available by anonymous FTP from
ftp.dcs.ed.ac.uk [129.215.160.5] in the directory
/pub/rasmol. The announcement was made in bionet.software,
bionet.announce, sci.bio, sci.chem,
comp.graphics.visualisation, bionet.xtallography
and sci.techniques.xtallography newsgroups.
rasmol-2.7.6.0/ChangeLog/ChangeLog.7 0000775 0000000 0000000 00000007201 13364034342 0016734 0 ustar 00root root 0000000 0000000 [10/10/96] RS render.c
Fixed bug in ReSize screen that incorrectly set MaxZoom. This
should match the code in InitialTransform(). Special Thanks
to Tim Maffet.
[10/10/96] RS pixutils.c
Correct bug testing incorrect OutCode in routine ClipLine().
Special thanks to Tim Maffet.
[07/10/96] RS raswin.c
Changed the style and class of the command line window to
allow it to be minimized in Windows 95. Thanks to Ken Davis.
[30/09/96] RS render.c
Fixed a bug displaying crystallographic unit cell. Very
Special Thanks to Wei Dong
[24/09/96] RS rasmol.c
Add support for several command line options including
"-width", "-height", "-noconnect" and "-port". Special
thanks to Ryan Hung for the WidthxHeight code.
[23/09/96] RS command.c
Modified the FetchFile function to trap SIGPIPE when calling
popen(3) to gunzip or decompress. Thanks to Guy Slater.
[17/07/96] RS command.c
Fixed a bug in RasWin under Windows 95 that prevents
filenames from containing spaces. Thanks to Bob Long.
[16/07/96] RS transfor.c
Improved the implementation of ScaleColourMap that no
longer uses floating point values. This fixes problems
on IBM PC and improves performance.
[16/07/96] RS command.c
Add the "set sequence " command to RasMol and
implemented "DescribeSequence" that controls whether "show
sequence" displays three-letter or one-letter amino codes.
[16/07/96] RS pixutils.c
Fixed 16bit overflow problem when display polygons in
RasWin in routines "DrawPolygon" and "ClipPolygon".
[02/07/96] RS x11win.c
Fixed a bug in RasMol that treated the SGI NumLock key as
an Alt-modifier. Popping up menus when typing into the
canvas window. Thanks to Andrew Leach and Ryan Smith.
[01/07/96] RS rasmac.c
Corrected problems in "OpenDialogHook" and "SaveDialogHook"
that caused several problems including a system crash when
running Symmantec Directory Assistance II. Special Thanks
to Kevin E. Gilbert (for the patch) and Henry Rzepa (for
discovering the problem).
[07/05/96] RS command.c
Corrected bug in "ExecuteSetCommand" that caused "set backfade"
to always reset "set transparency" (a missing break statement).
Special Thanks to Tim Maffett.
[09/04/96] RS script.c
Modified the generation of script files to fix a bug in
writing the "colour axes" command to include commas. Special
to Guy Slater.
[29/03/96] RS script.c
Modified the generation of script files to avoid writing
"colour ribbons none" at each residue, which is the default.
Thanks to Alan Lewis.
[21/11/95] RS command.c
Changed the conditions in FetchFile on when RasMol determines
bonds itself to the condition "bonds < atoms-chains". This
allows multiple connected fragments. Thanks to William Hart.
[10/11/95] RS infile.c x11win.c
Made several #ifdef VMS changes to allow RasMol to compile
with VAX C. Thanks to Gail Schuman.
[10/11/95] RS pixutils.h pixutils.c repres.c
Changed the field names hx, hy and hz in structure Knot to
to dx, dy and dz to avoid clash with predefined AIX macro hz.
Thanks to Hiroki Morizono.
[09/11/95] RS transfor.c
Fixed bug in ApplyTransform() that caused RasMol to crash if
all atoms have the same co-ordinates. Thanks to Guy Slater.
[06/11/95] RS script.c
Fixed bug in RasMol script generation that outputs the
background colour before the zap command (which resets
the background colour to black). Thanks to Niels Kristian
Bech Jensen.
[20/10/95] RS infile.c
Fixed bug in RasMol CHARMm file format reader. RasMol now
uses the standard PDB residue numbering in column 56, rather
than the sequential numbering in column 5. Thanks to Milan
Hodoscek
rasmol-2.7.6.0/ChangeLog/ChangeLog.8 0000775 0000000 0000000 00000012144 13364034342 0016737 0 ustar 00root root 0000000 0000000 [24/2/99] HJB Release of RasMol_2.6_CIF(Rev 2) at
http://www/bernstein-plus-sons.com/software/rasmol
and announce to mailing lists.
[21/2/99] HJB cif.h
Add prototypes of cif_make_handle, cif_read_file,
cif_make_file, cif_save_character to avoid compiler warnings
[21/2/99] HJB cif_ctonum.c
Remove unneeded values.h
[21/2/99] HJB cif_ctonum.h
Correct prototype
[21/2/99] HJB infile.c
Add cif_ctonum.h, define LoadCIFMolecule prototype,
initialize ch, add return to avoid compiler warnings.
[21/2/99] HJB abstree.c, cif.c, cif_ctonum.c, command.c,
infile.c, molecule.c
Use string_case.h instead of for IBMPC,
VMS and APPLEMAC.
[21/2/99] HJB rasmol.h
Update version, add some definitions from R. Sayle's
2.6.4 in preparation for 2.7.0.
[21/2/99] HJB rasmac.c, rasmol.c, raswin.c
Update reported date on startup.
[21/2/99] HJB render.c
Add cif_fract.h to avoid compiler warnings.
[21/2/99] HJB string_case.c
Replace garbled version, provide string_case.h.
[21/2/99] HJB script.c
Initialize first, last, radius, to avoid compiler warnings
[21/2/99] HJB transfor.c
Initialize min and max to avoid compiler warnings.
[10/1/99] HJB Release of RasMol_2.6_CIF(Rev 1) at
http://www.bernstein-plus-sons.com/software/rasmol
and announce to mmCIF mailing list.
[9/1/99] HJB cif.c
Change toupper calls to ToUpper calls.
[8/1/99] HJB command.c
Add argument to CreateMoleculeBonds to force zapping
on connect.
[8/1/99] HJB infile.c
Log requested bonds which cannot be made in NullBonds
and report to users, add RightJustify to right-justify
residue names, recognize _atom_site_disorder_group
for small molecule alternate conformerse, recognize bonds
which don't have either atom names or atom numbers.
[8/1/99] HJB molecule.c
Add argument to CreateMoleculeBonds to force zapping
on connect.
[8/1/99] HJB molecule.h
Add argument to CreateMoleculeBonds to force zapping
on connect, add NullBonds to log requested bonds which
cannot be made.
[8/1/99] HJB mswin31.c
Use VERSION to construct window title.
[8/1/99] HJB outfile.c
Use VERSION to construct Postscript output file header.
[8/1/99] HJB rasmac.c
Use VERSION to report version on startup.
[8/1/99] HJB rasmol.c
Use VERSION to report version on startup.
[8/1/99] HJB raswin.c
Use VERSION to report version on startup.
[8/1/99] HJB script.c
Use VERSION to construct various output file headers.
[8/1/99] HJB x11win.c
Use VERSION to construct window title.
[22/12/98] HJB Preliminary release of RasMol_2.6_CIF at
http://www.bernstein-plus-sons.com/software/rasmol
[19/12/98] HJB command.c
correct handling of internal help files under windows,
and allow for unix help files on a mac.
[18/12/98] HJB Makefile.in, Imakefile
Update for CIF support.
[09/12/98] HJB infile.c
Cummulative changes for fractional coordinates,
CIF.
[09/12/98] HJB command.c
Changes for alt, model labels, colour schemes,
CIF.
[09/12/98] HJB molecule.h
Cummulative changes for fractional coordinates,
new colour schemes, CIF.
[09/12/98] HJB molecule.c
Cummulative changes for fractional coordinates,
new colour schemes, CIF.
[09/12/98] HJB x11win.c
Update comments, menus and version text.
[09/12/98] HJB mswin31.c
Update comments, output file commentary.
[09/12/98] HJB outfile.c
Update comments, output file commentary.
[09/12/98] HJB script.c
Update comments, output file commentary.
[09/12/98] HJB rasmol.c
Update comments, output file commentary.
[04/12/98] HJB pixutils.c
Update comments, code to stripe bonds for alternate
conformers.
[04/12/98] HJB pixutils.h
Update comments, protytpes to stripe bonds for alternate
conformers.
[04/12/98] HJB rasmac.c
Update comments, adjust code for current Metrowerks
compiler.
[04/12/98] HJB raswin.c
Update comments, adjust code for current Metrowerks
compiler.
[04/12/98] HJB tokens.h
Update comments, tokens for alt, model colours.
[04/12/98] HJB transfor.c
Update comments, add code for alt, model colours.
[04/12/98] HJB transfor.h
Update comments, prototypes for alt, model colours.
[23/11/98] HJB abstree.c
Add code for %A, %M specifiers, divide u/l case.
[22/11/98] HJB cif_fract.c
New routine, derived from cif2pdb by H.J. Bernstein
and F. C. Bernstein.
[22/11/98] HJB cif_fract.h.
New header for cif_fact.c.
[22/11/98] HJB cif_stx.c
New routine, derived from P. Ellis CBFlib parser.
[23/11/98] HJB render.c
Update comments, add code to stripe bonds for alternate
conformers.
[23/11/98] HJB repres.c
Update comments, add code to stripe bonds for alternate
conformers.
[09/09/98] HJB cif_ctonum.c
New routine, derived from ciftbx by S. R. Hall
and H. J. Bernstein.
[09/09/98] HJB cif_ctonum.h
New header for cif_ctonum.c.
[18/08/98] HJB cif.h
New header for cif.c, derived from CBFlib by P. Ellis
and H. J. Bernstein.
[18/08/98] HJB cif.c
New routine derived from CBFlib by P. Ellis and
H. J. Bernstein.
[14/08/98] HJB rasmol.c
Added hooks for termio for Linux. These changes
are similar to, but not identical to the FreeBSD hooks.
See the linux conditionals.
rasmol-2.7.6.0/ChangeLog/ChangeLog.9 0000664 0000000 0000000 00000251343 13364034342 0016743 0 ustar 00root root 0000000 0000000 RasMol 2.7.5
Molecular Graphics Visualisation Tool
13 June 2009 (rev. 17 July 2009)
Based on RasMol 2.6 by Roger Sayle
Biomolecular Structures Group, Glaxo Wellcome Research & Development, Stevenage, Hertfordshire,
UK
Version 2.6, August 1995, Version 2.6.4, December 1998
Copyright (c) Roger Sayle 1992-1999
and Based on Mods by
+---------------------------------------------------------------------------------------------+
| Author | Version, Date | Copyright |
|----------------------+---------------------------------+------------------------------------|
| Arne Mueller | RasMol 2.6x1 May 1998 | (c) Arne Mueller 1998 |
|----------------------+---------------------------------+------------------------------------|
| Gary Grossman and | RasMol 2.5-ucb November 1995 | (c) UC Regents/ModularCHEM |
| Marco Molinaro | RasMol 2.6-ucb November 1996 | Consortium 1995, 1996 |
|----------------------+---------------------------------+------------------------------------|
| Philippe Valadon | RasTop 1.3 August 2000 | (c) Philippe Valadon 2000 |
|----------------------+---------------------------------+------------------------------------|
| Herbert J. Bernstein | RasMol 2.7.0 March 1999 | (c) Herbert J. Bernstein 1998-2008 |
| | RasMol 2.7.1 June 1999 | |
| | RasMol 2.7.1.1 January 2001 | |
| | RasMol 2.7.2 August 2000 | |
| | RasMol 2.7.2.1 April 2001 | |
| | RasMol 2.7.2.1.1 January 2004 | |
| | RasMol 2.7.3 February 2005 | |
| | RasMol 2.7.3.1 Apr 06 | |
| | RasMol 2.7.4 Nov 07 | |
| | RasMol 2.7.4.1 Jan 08 | |
| | RasMol 2.7.4.2 Mar 08 | |
| | RasMol 2.7.5 Jun 09 RasMol | |
| | 2.7.5.1 Jul 09 | |
+---------------------------------------------------------------------------------------------+
This Release by
Herbert J. Bernstein, Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
yaya@bernstein-plus-sons.com
Copyright (c) Herbert J. Bernstein 1998-2009
-----------------------------------------------------------------------------------------
THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS
***** USE WITH CAUTION ******
-----------------------------------------------------------------------------------------
IMPORTANT
This version is based directly on RasMol 2.7.4.2, RasMol 2.7.4.1, RasMol 2.7.4, RasMol
2.7.3.1, RasMol 2.7.3, RasMol 2.7.2.1.1 and on RasMol 2.7.2, on RasMol 2.7.1.1, on RasTop
1.3, on RasMol version 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version 2.6.4, and
RasMol 2.5-ucb and 2.6-ucb. Please read the file NOTICE for important notices which apply
to this package and for license terms (GPL or RASLIC).
This version of RasMol is not in the public domain, but it is given freely to the
community in the hopes of advancing science. If you make changes, please make them in a
responsible manner, and please offer us the opportunity to include those changes in
future versions of RasMol.
-----------------------------------------------------------------------------------------
Changes from RasMol 2.7.4.2 to RasMol 2.7.5 include:
* Support for SBEVSL movie commands.
* Support for Lee-Richards surface approximation by contouring pseudo-Gaussian electron
densities.
* Selection of atoms by proximity to map contours
* Coloring of maps by the colors of neighboring atoms
* Signficant improvements to the GTK version by Teemu Ikonen
Changes to RasMol 2.7.4.2 to create RasMol 2.7.5.1:
[18/07/2009] HJB .symlinks
Update .symlinks to 2.7.5
[17/07/2009] HJB cif.c command.c raswin_install.nsi
Windows port changes: Update NSIS installer script
Change from mktemp to tmpfile and use rewind not freopen
[17/07/2009] HJB rasmol.doc rasmol.hlp rasmol.html cif.c command.c
rasmol.man rasmol.tex rasmol.vms raswin.rtf
Update doc for 2.7.5, and fix some spacing
[17/07/2009] HJB cif.c x11win.c
Correct X11 file menu for more than 5 open files
Correct cif_read_file CBFlib version to use a temporary file
[16/07/2009] HJB rasmol_install.sh
Correct reporting of font installs for Chinese.X and Japanese.X
[14/07/2009] HJB transfor.c
Fix missing scaling in new translate logic
[12/07/2009] HJB command.c command.h tokens.c trnasfor.c transfor.h
Preliminary movie play logic.
[11/07/2009] HJB command.c
Switch record templates to SSSSSS as per manual
Fix a bug in defer symbol linking
Report undefined symbols in calls to show defer symbol
[10/07/2009] HJB Imakefile_base command.c
Correct Imakefile_base
Add defer/execute movie interaction
[09/07/2009] HJB Imakefile_base rasmol_build_options.sh
Provide new script, rasmol_build_options.sh to reconstruct
new Imakefile from stable Imakefile_base
[09/07/2009] HJB Imakefile rasmol.c
Default Imakefile to use local copies of CQRLIB, CVECTOR,
XFORMSLIB and CBFLIB.
Change from use of fl_init to fl_initialize for xforms-1.0.91
[08/07/2009] HJB Imakefile abstree.c applemac.c cif.stx.tab.c cmndline.c
command.c command.h graphics.h gtkwin.c multiple.c
outfile.c rasmac.c rasmol.c rastxt.c raswin.c render.c
repres.c transfor.c transfor.h wbrotate.c wbrotate.h x11win.c
Partial changes for defer/execute command.
Update versions of external files used in Makefile.
Cleanup of varibables names for saving dial values.
[04/07/2009] HJB command.c maps.c molecule.c pixutils.c rasmol.h repres.c
transfor.c
Clean up errors in map color atom command and remove use
of polys with differing vertex colors by breaking up the
triangles into monchrome subtriangles
[02/07/2009] TPI molecule.c
Add #define _GNU_SOURCE to get the correct definition of basename()
[29/06/2009] HJB command.c
Fix to map select atom add
Add esd to map show for distances to surfaces
and make code for distances to reentrant surfaces more accurate
[25/06/2009] HJB Imakefile command.c molecule.c molecule.h
Update to use of NearTree 2.1.2
Add code to report surface fit stats in map show
[18/06/2009] HJB Imakefile build_MACOSX.sh build_all.sh command.c
rasmol_install.sh tokens.c tokens.h
Add 'add' and 'within' parameters to map select atoms command
Also allow search radius to be specified
[16/06/2009] HJB Imakefile
Update Imakefile for use of installed packages
[14/06/2009] HJB Imakefile
Set up loads of necessary external packages from sourceforge
[13/06/2009] HJB Imakefile applemac.c cmndline.c cmndline.h command.c
graphics.h maps.h molecule.c molecule.h mswin31.c
multiple.c rasmac.c tokens.c tokens.h transfor.c transfor.h
x11win.c
Integrate surface and movie code with gtk code
[03/06/2009] TPI rasmol.c
DisplayUsage(): Revert back to fputs
[27/05/2009] TPI render.c
Do not assume sizeof(Pixel) == sizeof(Long)
Use variables of type Pixel consistently in buffer clearing functions.
Remove version of ClearBuffers() which does not require memset().
[17/07/2009] TPI graphics.h
add startup representation flags
[17/07/2009] HJB rasmol.doc rasmol.html rasmol.man,
Update manual to 2.7.5
[12/05/2009] TPI gtkwin.c
Fix vte input problems by using vte input callback instead of
g_io_watch.
Various file open fixes to GTK version
Fix setting of initial window size.
Fix file open in GTK version: Copy the file name to global var
DataFileName before calling FetchFile.
Add file type filtering to GTK filechooser.
Whitespace fixes.
[12/05/2009] TPI rasmol.c
Fix text output with VTE in GTK interface.
[12/05/2009] TPI command.c command.h rasmol.c
Refactor file opening code. Add support for opening more
than one file from the command line.
Simplify file opening code, remove globs and allow to open files
with spaces and other 'special' characters.
Fix reading files from stdin with '-' arg.
[07/02/2009] HJB command.c command.h rasmac.c rasmol.c rastxt.c raswin.c
tokens.c tokens.h transfor.c transfor.h
Updates to enable the record mode to files. Use with caution,
there are some problems with picking up ReDrawFlag on changes
in appearance. Mouse motion helps to get past the glitch.
[06/02/2009] HJB command.c command.h graphics.h gtkwinc. maps.c rasmac.c
rasmol.c rastxt.c raswin.c tokens.c tokens.h transfor.c
transfor.h
First pass at SBEVSL movie-making commands
[16/11/2008] HJB command.c maps.c
Update to Lee-Richards approximation for probe of given
probe radius with new logic for map spread 0; map scale off;
so that set radius ; map resolution .67; map spread 0;
map scale off; map generate surface produces a good surface
approximation
[20/05/2009] TPI molecule.c
ReviseTitle(): If no identcode, use filename in the title
[20/05/2009] TPI gtkwin.c multiple.c
Update GTK molecule list when a molecule is picked
gtkwin.c: set_gtk_open_file(); new function.
UpdateGtkMoleculeList(); free allocated lists, reindent
multiple.c: SelectMolecule(); call set_gtk_open_file()
[20/05/2009] TPI gtkwin.c rasmol.c
Fix recent files support in GTK version
build_gtkmenu(): Set recent user sort type to most recently used.
Display 30 recent files.
Reindent.
[20/05/2009] TPI printing-resolution.glade sizechooser.glade
Remove useless response_id properties from glade files
[18/05/2009] TPI gtkwin.c rasmol.c
Really fix VTE output in GTK version.
Stop using PTYs for terminal io with VTE.
Don't touch the controlling terminal during init and reset.
Make Delete key work and ignore unhandled terminal escape sequences.
Use custom versions of RasMolExit and RasMolFatalExit in GTK version.
Add some keyboard shortcuts to the GTK GUI.
[18/05/2009] TPI gtkwin.c
Change image export shortcut to C-X
[14/05/2009] TPI rasmol_48x48.xpm Imakefile gtkwin.c
Add an xpm icon for Rasmol.
Set window icon in the GTK version.
[13/05/2009] TPI command.c
revert the filename globbing and extension handling code
[15/02/2009] HJB rasmac.c rasmol.c raswin.c
Clean up handling of ReDrawFlag for appearance changes
[31/10/2008] HJB command.c maps.c
First pass a Lee-Richards surface approximation for map
generate with map resolution 1; map cale off; map level .5;
map generate mesh
Changes from RasMol 2.7.4.1 to RasMol 2.7.4.2 include:
* Alignment of command line sizing and positioning options for Windows and X-Windows
version. The command line options -height nnnn, -width nnnn, -xpos nnnn and -ypos
nnnn may be used to set the size and position of the initial window.
* Change of the encoding for Japanese messages and menus from SJIS to EUC-JP, and
corrections to the fontset handling for Chinese and Japanese. Thanks to Mamoru
Yamanishi for contributing the improved fontset logic.
* Updates to the rasmol_install.sh and rasmol_run.sh scripts to support Chinese and
Japanese using cxterm.
* Optional use of GTK. Thanks to Teemu Ikonen for the new GTK code.
Changes to RasMol 2.7.4 to create RasMol 2.7.4.1:
[18/03/2008] HJB graphics.h mswin31.c rasmol.c rastxt.c
raswin.c x11win.c
Add global InitWidth, InitHeight, InitXPos, InitYPos
to support common implementation of command line
options -height nnnn -width nnnn -xpos nnnn -ypos nnnn
to control initial window size and position
[18/03/2008] HJB x11win.c
Redo Japanese and Chinese fontset logic as per suggestion
by Mamoru Yamanishi
[18/03/2008] HJB Imakefile
Allow use of old X locale.
[18/03/2008] HJB langsel_unix.c
Switch Japanese for unix from SJIS to EUC-JP, introducing
langsel_unix.c
[21/02/2008] TPI actionmenu.gtk egg-macros.h eggfileformatchooser.c
eggfileformatchosser.h graphics.h gtkwin.c Imakefile
multiple.c printing-resolution.glade rasmol.c sizechooser.glade
transfor.c wbrotate.c
Addition of GTK interface by T. Ikonen, including new routines
actionmenu.gtk egg-macros.h eggfileformatchooser.c
eggfileformatchosser.h gtkwin.c printing-resolution.glade
sizechooser.glade
Changes from RasMol 2.7.3 to RasMol 2.7.4.1 include:
* Support for maps.
* Message and menu translations for Russian, Bulgarian, Japanese and Chinese. Our
thanks to G. Pozhvanov, G. Todorov, Nan Jia, Mamoru Yamanishi and Katajima Hajime.
* Fix torsion angle calculation as per bug report and patch by Swati Jain.
* Corrections by Ladislav Michnovic to port to more platforms.
* Code to read remediated PDB entries as suggested by Huanwang Yang
* Updated icons.
* Extended export menus.
Changes to RasMol 2.7.4 to create RasMol 2.7.4.1:
[19/01/2008] HJB
Release 2.7.4.1 created
[18/01/2008] HJB command.c, maps.c, maps.h, molecule.c
mswin31.c outfile.c outfile.h pixutils.c pixutils.h
rasmac.c, repres.c
Add LoadCCP4MapFile. Extend range of stereo angle to
60 degrees. Add GM notoggle command. Add code to
avoid trying to reuse a zapped map. Increase default
map resolution to 1 Angstrom. Change mapdata to
void * and use memmove to allow multiple data types,
add fields for number of grid divisions, map type,
element size and element type. Add code to load
and save maps in CBFlib format. Fix stereo.
[16/01/2008] HJB vector.c wbrotate.c
Fix multiple definitions of PI.
[14/01/2008] LM infile.c
Add include of string.h as per Ladislav Michnovic.
[14/12/2008] HJB graphics.h
Add buffers for slab and depth pixel-by-pixel
cutoff values.
[10/12/2007] GM langsel.c langsel.h languages/README.txt
languages/genlanselall languages/langsel*.utf.c,
tokens.c tokens.c
Corrected japanese langsel encoding. It is now
Shift_JIS.Added messages for NoToggle and ColourMode
commands. Updated langsel README.txt. Add NoToggle
and ColourMode commands
[06/12/2008] GM command.h
Add NoToggle and ColourMode variables.
[25/11/2007] HJB cif_fract.c
Rewrite calculation of matrix inverse.
Changes to RasMol 2.7.3.1 to create RasMol 2.7.4:
[19/11/2007] HJB
Release 2.7.4 created
[19/11/2007] HJB abstree.c abstree.h
Break out element identification from GetElemNumber
into GetElemDescrNumber. Fix torsion angle calculation
as per bug report and patch by Swati Jain.
[19/11/2007] HJB applemac.c
Add code to make languages sticky. Add register and
donate menu items, make languages sticky and launch
browsers.
[19/11/2007] HJB cif_fract.c
Correct calculation of matrix transforming orthogonal
to fractional coordinates and rewrite matrix
transforming fractional to orthogonal.
[19/11/2007] HJB command.c command.h
Add code for map commands. Make CommandError accessible
from other routines. Add Raster3D write/save option.
Allow proberadius of 6 Angstroms. Add Bulgarian,
Chinese, Japanese and Russian commands. Allow
spacefill up to 12 Angstroms. Allow mirror and
rotate suboptions on write/save.
[19/11/2007] HJB font.h, graphics.h
Allow access to font parameters and support info
[19/11/2007] HJB Imakefile
Add use of CBFlib
[19/11/2007] HJB infile.c
Make sensitive to PDB version to allow for handling of
remediated files, based on changes suggested by
Huanwang Yang of the RCSB PDB in April 2007.
[19/11/2007] GT langsel.c languages/
langsel.c restructured to be generated from separate
language files in the directory languages/
[19/11/2007] HJB molecule.c molecule.h
Add atom type processing and DA, DC, DG, DT, DI for
remediated PDB DNAs, based on changes suggested by
Huanwang Yang of the RCSB PDB in April 2007.
[19/11/2007] HJB multiple.c multiple.h
Manage map data for multiple molecules. Increase the number
of molecules from 5 to 15. Increase the number of characters
in the name to 33 characters.
[03/12/2006] HJB outfile.c
Clean up compilation warnings in outfile.c
[19/11/2007] HJB outfile.c outfile.h
Add Raster3D support based on code by V. Stanev. Partial
Vector PS map support.
[19/11/2007] HJB pixutils.h
Fix stereo of ribbons and map surfaces. Protect against
duplicate definition of Knot struct. Make ClipPolygon
accessible.
[19/11/2007] HJB rasmac.c rasmac.h
Increase terminal window to 132 characters. Add About dialog.
Clean up maps on exit. Add support for Russian, Bulgarian,
Chinese and Japonese. Add register and donate browser calls.
Add G4 CPU type. Extend export file types.
[19/11/2007] HJB RasMac.r
Update icons to new style. Extend Export menu to BMP...,
GIF..., IRIS RGB..., PPM..., Sun Raster, PostScript, PICT...,
Vector PS ..., Molscript ..., Kinemage ..., POVRay 3 ...,
VRML ..., Ramachandran ..., Raster3D ..., RasMol Script ....
Extend Apple menu to About RasMol..., RasMol Help ...,
Register ..., Donate ....
[19/11/2007] HJB rasmol.c
Update to release 2.7.4 with map support.
[19/11/2007] HJB script.c script.h
Add code to write out scripts for maps.
[19/11/2007] HJB string_case.c string_case.h
Fix case sensistive of last character comparison of strcasecmp and
strncasecmp. Add str255casecmp, strcasestr.
[19/11/2007] HJB tokens.c tokens.h
Add tokens for Average (MeanTok), Bulgarian (BulgarianTok),
Chinese (ChineseTok), Contour (ContourTok = LevelTok),
Generate (GenerateTok), Japanese (JapaneseTok), Level (LevelTok
= ContourTok), Map (MapTok), Mask (MaskTok), Mesh (WireframeTok),
Mirror (MirrorTok), New (NewTok), Next (NextTok), R3D or
Raster3D (Raster3DTok), Resolution (ResolutionTok), Spacing
(SpacingTok), Spread (SpreadTok), Width (SpreadTok),
[19/11/2007] HJB transfor.c transfor.h
Add map point colouring routines, ColourPointAttrib and
ColourPointPotential.
[19/11/2007] HJB x11win.c
Extend Export menu to BMP ..., GIF ..., IRIS RGB ..., PPM ...,
Sun Raster, PostScript, PICT ..., Vector PS ..., Molscript ...,
Kinemage ..., POVRay 3 ..., VRML ..., Ramachandran ...,
Raster3D ..., RasMol Script .... Enable and extend Help
menu to About RasMol..., User Manual..., Register...,
Donate.... Set locale for each langauge and use fontsets.
Use table of languages versus fonts in langsel. Add
About splash screen and revise popup logic to handle it.
Change text metrics to allow for Chineses and Japanese.
Try to make lack of access to shared memory non-fatal.
[03/10/2007] PK molecule.c
"RasMol - " string added to the title of the window.
[03/10/2007] PK multiple.c
Window title is updated when different molecule is selected.
[02/02/2007] HJB rasmol.c
Remove // comments for AIX build. Fix signed length conflict
[01/03/2007] GT rasmol.c
Chinese version.
[23/12/2006] HJB x11win.c
Detect remote X server that does not share memory
[29/12/2006] HJB rasmol.c x11win.c
Update x11win.c and rasmol.c to add links to list of browsers
and to kill About dialog when the menu bar is selected
[29/12/2006] HJB rasmol_install.sh
Update rasmol_install.sh to allow recompilation of fonts
on install to handle openwin and other old systems that
can't handle byte-swapped bdf files, and add enviroment
variable RASMOL_NOSPAWN to suppress spawn in intermediate
xterm from rasmol_run.sh. -- HJB
[23/12/2006] HJB rasmol_install.sh, rasmol_run.sh scripts
Add new rasmol_install.sh and rasmol_run.sh scripts
[29/11/2006] HJB raswin.idm
Fix missing raswin.idm in src.
[29/11/2006] HJB rasmol.c
Add missing include of sys/stat.h in rasmol.c
[10/12/2006] HJB x11win.c
Additional updates for linux build with Russian, cleaning
up X11 font selection for CP1251 and recovering when fonts
are missing. -- HJB
[03/12/2006] HJB x11win.c
Mods for about screen under Linux -- HJB
[28/11/2006] HJB x11win.c
Changes for Russian and About dialog in unix
[20/10/2006] HJB wbrotate.c
Localize " not found!" message in RemoveBond and CreateBondAxis
[16/09/2006] HJB x11win.c rasmol.c
Start of RasMol Russian Translation Project based on translations
by Gregory A. Pozhvanov of Saint Petersburg State University.
[11/02/2006] HJB script.c script.h
Add mirror and rotate options for VRML.
Changes from RasMol 2.7.2.1.1 (the final reference release of RasMol 2.7.2) to RasMol 2.7.3.1
include:
* Adjustment to the mouse handling for a better, more natural feel. Our thanks to C.
Chigbo for the suggestion.
* Correction to cif.c for blanks after an initial quote mark.
* Correction to mswin31.c to restore lost initializations of ZRange and
DialValue[8..9].
* Modifications by Mamoru Yamanishi to Imakefile and rasmol.c to use xforms for GUI
file open. This patch needs the opens source xforms 1.0.90 library by Steve Lamont.
* Correction to molecule.c to correct input of xyz files. Thanks to Stuart Prescott.
* Revision to CPK colors by C. Chigbo. The new colors are called CPKNEW. The current
CPK colors remain available as CPK.
* Correction to negative torsion angle monitors and to imprecise distance and angle
monitors by C. Chigbo. This patch corrects the display of negative torsion angles
caused by use of the unsigned short type, and correctys imprecise distance and angle
displays. This extends the original patch which was just for torsion angles
(torsion.patch). A side effect of this change is to limit the available range for
distance monitors to approximately 327 AAngstroms.
* Initial code for display of solid Lee-Richards molecular surfaces. This patch adds
the basic code for display of Lee-Richards surfaces with a new Molecular Surface menu
item, and surface molecule and surface solvent
commands.
* Corrections of ribbons 0, etc. commands by R. Chachra. With this patch, the wireframe
0, ribbon 0, cartoon 0, backbone 0, strands 0 and trace 0 commands work the same as
these command with off instead of 0.
Changes to RasMol 2.7.3 to create RasMol 2.7.3.1:
[21/04/2006] HJB rasmol.h RasMac.r raswin.rc
Update version to 2.7.3.1
[21/04/2006] CC abstree.c render.c repres.c repres.h
Fix by Clarice Chigbo to improve accuracy of
distance calculations by changing from Long to
double. Report model number. Use Long instead
of short for monitors.
[15/12/2005] HJB x11win.c
Fix mouse runaway by removing conflict of HeldStep
and HeldButton variable name use.
[16/07/2005] HJB abstree.c infile.c render.c
Correct sign errors in use of ztrl
Changes to RasMol 2.7.2.1.1 to create RasMol 2.7.3:
[06/02/2005] HJB
Release 2.7.3 created
[21/01/2005] HJB molecule.c
Correct XYZ input by capping atom types. Thanks to
Stuart Prescott.
[16/01/2005] HJB applemac.c, cmndline.c, command.c, command.h,
infile.c, langsel.c, langsel.h, langsel_mac.c,
molecule.c, molecule.h, mswin31.c, multiple.c,
pixutils.c, pixutils.h, rasmac.c, rasmol.c,
rastxt.c, raswin.c, render.c, render.h, repres.c,
repres.h, tokens.c, tokens.h, transfor.h, x11win.c
Base level of changes for Lee-Richards molecular
surfaces.
[12/01/2005] Clarice Chigbo repres.c, render.c, repres.h
Correction to negative torsion angle monitors and to imprecise
distance and angle monitors; limits the available range for
distance monitors to approximately 327 Angstroms.
[17/01/2005] Clarice Chigbo script.c
Output CPKNEW in scripts
[04/01/2005] Ricky Chachra command.c
Fix to wireframe 0, ribbon 0, cartoon 0, backbone 0,
strands 0 and trace 0 commands to work the same as these
command with off instead of 0
[30/10/2004] Mamoru Yamanishi Imakefile, rasmol.c
Used xforms to provide GUI for file open under X-windows
[21/10/2004] Clarice Chigbo tokens.c, tokens.h
Define CPKNEW token
[20/10/2004] Clarice Chigbo transfor.c, transfor.h
New CPK color table
[26/04/2004] HJB cif.c
correction to handling of blank immediately following
initial quote mark.
[26/04/2004] HJB vector.c
correction to SubtractAtoms for bond rotation.
Changes from RasMol 2.7.1 (the final reference release of RasMol 2.7.2) to RasMol 2.7.2.1.1
include:
* Post release patches to command.c were included to fix the handling of load inline in
the UCB multiple molecule environment. In addition conditional code controlled by
STRICT was disabled to restore operation of load inline under windows. Thanks to Jan
Reichert for pointing out these problems. Thanks to E. Martz
for pointing out an error in the Spanish translation
credits which has been corrected. Thanks to a report by Julien Hering, the omission
of a prior fix to the MS Windows version was found and corrected on 7 May 2004.
* Adaption of the multilingual mods from RasMol 2.7.1.1 into Rasmol 2.7.2.1.
* Rewrite of the mouse handling and rotation logic to correct the problems in 2.7.2 and
make the feel of 2.7.2.1 closer to that of RasMol 2.7.1.
* Addition of French menus and messages
* Addition of Italian menus and messages
* Adoption of picking for selection of atoms, groups or chains from RasTop 1.3.
* Adoption of backclipping from RasTop 1.3
* Adoption of shadepower command for glassy surfaces from RasTop 1.3
* Change of the menu stereo option to rotate cross-wall-none
* Allow longer atom names (12 characters) in CIFs.
* Incorporation of some of the code from the UCB RasMol variants. Out thanks to Eileen
Lewis and Marco Molinaro for their cooperation in contributing the UCB Enhanced
RasMol code for incorporation into the RasMol 2.7 series.
* Code to represent bonds in and to alternate conformers with a narrowed portion in the
middle of each bond.
* An attempt to fix some of the chirality reversals in some of the output modes.
* Fixes for some of the problems reported since the last release.
Post-release changes to RasMol 2.7.2.1.1:
[07/05/04] HJB mswin31.c
restored lost fix for intialization of ZRange and
DialValue[8..9] and rebuilt raswin.exe. Thanks to
Julien Hering.
[14/02/04] HJB pixutils.c
remove static from declaration of ClipVector.
[14/02/14] HJB cif_stx.c
remove trailing characters from #endif.
[03/02/04] HJB Makefile.in
Change transfer to transfor in 2 dependencies. Thanks
to R. Harlow.
Changes to RasMol 2.7.2.1 to create RasMol 2.7.2.1.1:
[26/01/04] HJB abstree.c
Fix warning on sprintf calls with unused args, match long
variables with %ld format descriptors.
[26/01/04] HJB cif.c
Add brackets to avoid compiler warnings on dangling elses.
Fix cif_lex to parse 'O''' correctly. Change from
WORD to CIFWORD to avoid conflict with windows.h.
[26/01/04] HJB cif.h
Change from WORD to CIFWORD to avoid conflict with windows.h.
Add prototype for cif_free_handle.
[26/01/04] HJB cif.stx.tab.c
Change from WORD to CIFWORD to avoid conflict with windows.h.
[26/01/04] HJB cif_ctonum.c
Remove unused variable dndec
[26/01/04] HJB cif_fract.c
Remove unused variable kk
[26/01/04] HJB cif_stx.c
Change from WORD to CIFWORD to avoid conflict with windows.h.
Add include of rasmol.h.
[26/01/04] HJB command.c
Initialize variables to avoid compiler warnings. Use %ld
format for long variables. Fix RotMode == RotBond which
should have been an assignment. Add parens on logical
expressions.
[26/01/04] HJB command.h
Add prototypes for ResumePauseCommand, InterruptPauseCommand.
[26/01/04] HJB graphics.h
Add include of windows.h
[26/01/04] HJB infile.c
Removed unused ReadValue2. Add brackets to avoid compiler
warnings on dangling elses. Initialize variables to avoid
compiler warnings.
[26/01/04] HJB langsel.c langsel_mac.c
Add include of string.h
[26/01/04] HJB molecule.c
Add include of graphics.h. Change to %ld format for longs.
Remove unused variables. Add brackets to avoid compiler warnings
on dangling elses.
[26/01/04] HJB molecule.h
Add prototype of TestDisulphideBridge.
[26/01/04] HJB multiple.c
Fix reversed comment terminator. Add include of string.h. Add
brackets to initializer to match structure.
[26/01/04] HJB multiple.h
Add prototype of ReRadius.
[26/01/04] HJB outfile.c
Initialize variables to avoid compiler warnings. Change to %ld
for long.
[26/01/04] HJB pixutils.c
Initialize variables to avoid compiler warnings. Removed unused
variables.
[26/01/04] HJB pixutils.h
Add prototypes of DrawTwinLine, ClipLine, ClipTwinLine,
ClipDashLine, DrawTwinVector, ClipVector, ClipTwinVector,
ClipDashVector.
[26/01/04] HJB rasmol.c
Add parens to avoid compiler warning.
[26/01/04] HJB rasmol.h
Set version and date. Add include of stdlib.h for malloc.
[26/01/04] HJB render.c
Change the handling of very long longs to avoid a compiler
warning. Use %ld format for longs.
[26/01/04] HJB repres.c
Remove unused variables. Use %ld format for longs. Initialize
variables to avoid compiler warnings.
[26/01/04] HJB repres.h
Add prototype of LoadDotsFile.
[26/01/04] HJB script.c
Add include of string.h. Use %ld format for longs. Initialize
variables to avoid compiler warnings. Remove unused variables.
Fix sign of trailing bits on VRML z coordinates.
[26/01/04] HJB script.h
Add prototype of WritePOVRay3File.
[26/01/04] HJB tokens.h
Add parens in definition of IsImageToken.
[26/01/04] HJB transfor.c
Add parens for logical expression. Remove unused variables.
Initialize variables to avoid compiler warnings.
[26/01/04] HJB transfor.h
Add prototype of DefineShade, RMat2RV, RV2RMat.
[26/01/04] HJB wbrotate.c
Add include of cmndline.h. Remove unused variables. Initialize
variables to avoid compiler warnings. Use %ld format for longs.
Add value for a returns that need them.
[26/01/04] HJB x11win.c
Initialize variables to avoid compiler warnings. Add brackets to
avoid compiler warnings on dangling elses.
[14/04/02] HJB Imakefile
Update to allow scripts to make multiple pixel depths by
setting PIXELDEPTH to 8, 16 or 32 externally. Add default
flags for various HP architectures.
[13/04/02] HJB cif.c
Reduce warnings by casting uses of size_t.
[13/04/02] HJB cif_ctonum.c
Reduce warnings by casting to int for pointers indptr-test.
[13/04/02] HJB command.c
Reduce warnings by explicit use of long (rather than Long)
for fpos, and casting to size_t for comparisons, etc.
[13/04/02] HJB infile.c
In ProcessPDBBond, match types of srcatm and dstatom by
changing from int to Long, casting to size_t for
comparisons, etc.
[13/04/02] HJB molecule.c
Change MemSize from int to size_t.
[13/04/02] HJB rasmol.c
Change AdviseLen from int to size_t, change socket to xsocket,
change __hpux to HPUX_LEGACY
[13/04/02] HJB rasmol.h
Add HPUX_LEGACY for old style hpux select.
[13/04/02] HJB render.c
Make test of sizeof(Long) > 4 conditional on not defining
_LONGLONG. Make some changes from Long to long, etc.
[13/04/02] HJB x11win.c
Cast some pointer diffs to int, change some Long to long,
etc.
[29/06/01] HJB command.c
Correct logic for inline load of a new molecule from
data file treated as a script.
[21/04/01] HJB all
Fix credit for initial Spanish translation. Thanks to
E. Martz.
[19/04/01] HJB command.c
Post release fix to handling of load inline in
windows version due to problem with STRICT logic.
Thanks to Jan Reichert for pointing
out the problem.
[18/04/01] HJB command.c
Post release fix to handling of load inline in UCB
multiple molecule environment. Thanks to Jan
Reichert for pointing out the
problem.
Changes from RasMol 2.7.1.1 and 2.7.2 to create RasMol 2.7.2.1:
[14/04/01] HJB script.c
Correct error in writing scripts with partial use of spacefill.
Thanks to Steven Vik for reporting the
problem.
[14/04/01] HJB rasmol.doc, itasmol2721.hlp, esrasmol.html
Updated manuals for 2.7.2.1.
[02/04/01] HJB abstree.c, abstree.h
Increase space for atom names from 4 to 12 characters.
[02/04/01] HJB applemac.c
Add symbolic ZRange, add 2 dials. See [12/01/01] changes for langsel.
[02/04/01] HJB cmndline.c, cmndline.h
Reworked all exits on mouse motion processing to leave values
in DialValues or WRot..., etc depending on RotMode. Made HeldButton
a global for future reference.
[02/04/01] HJB command.c, rasmol.c, rasmac.c, raswin.c
Change stereo command to cycle cross-wall-none.
[02/04/01] HJB command.c, script.c, transfor.c
Rework output of rotation information.
[02/04/01] HJB infile.c
Increase limit on atom names for CIF from 4 to 12 characters.
[02/04/01] HJB langsel.c langsel_mac.c
Add French (thanks to Jean-Pierre Demailly
) and Italian (Giuseppe Martini
and Giovanni Paolella
with contributions by: A. Davassi, M. Masullo, C. Liotto, G. Paolella,
G. Martini. Adapt to 2.7.2 menu structure.
[02/04/01] HJB mswin31.c
Removed "Printing Completed" message.
[02/04/01] HJB multiple.c
Save DotPtr to fix misplaced dots in multiple molecules. Save
LastTX, LastTY, LastTZ, LocalRadius, ShiftS, XlateCen. Make
"Insufficient memory" message be language dependent
MsgStrs[StrMalloc]
[02/04/01] HJB outfile.c, pixutils.c, repres.c
Rework backclipping separating ZOffset from new DepthValue,
define BitBack
[02/04/01] HJB tokens.c
Added the following tokens relative to 2.7.2, includes tokens
added for 2.7.1.1:
ASSE AxesTok
ASSI AxesTok
CADENA ChainTok
CADENAS ChainTok
CATENA ChainTok
CATENE ChainTok
COPY CopyTok
DEPTH DepthTok
DIBUJO CartoonTok
DIBUJOS CartoonTok
E AndTok
EJE AxesTok
EJES AxesTok
ELANCE BondTok
ELANCES BondTok
ELICHE HelixTok
ENGLISH EnglishTok
ELICHE HelixTok
ESQUELETO BackboneTok
ETIQUETA LabelTok
ETIQUETAS LabelTok
ETICHETTA LabelTok
ETICHETTE LabelTok
FILODIFERRO WireframeTok
FILDIFERRO WireframeTok
FILI StrandsTok
FRENCH FrenchTok
GIRO TurnTok
GIROS TurnTok
GRUPO GroupTok
GRUPPO GroupTok
HEBRAS StrandsTok
IMAGE ImageTok
ITALIAN ItalianTok
MOSTRAR DisplayTok
NASTRO RibbonTok
NASTRI RibbonTok
PASTE PasteTok
POSITION PositionTok
RIEMPIMENTO SpacefillTok
SALIR ExitTok
SCHELETRO BackboneTok
SELECTION SelectionTok
SHADEPOWER ShadePowerTok
SPANISH SpanishTok
TODO AllTok
TUTTO AllTok
VIEW ViewTok
VIGNETTA CartoonTok
VISUALIZZA DisplayTok
[02/04/01] HJB transfor.c
Rework interaction of mouse, local rotation and world rotation
to make horizontal mouse motion of individual molecule rotate
horizontally even when outer world rotation creates a tilt.
Restores incremental mouse motion effects similar to what
was in effect for 2.7.1, but with world rotations. Reworked
RasTop centering to restore 2.7.2 behavior -- defaults to
center the new rotation on the screen.
[02/04/01] HJB several
Make dial indices symbolic.
[02/04/01] HJB wbrotate.c, wbrotate.h
Rework interaction of mouse and world rotation to make
horizontal mouse motion of individual molecule rotate horizontally
even when outer world rotation creates a tilt.
Changes adopted from RasTop 1.3 in creating RasMol 2.7.2.1:
Note: These mods do not reflect the complete source of RasTop 1.3.
[31/01/00] PV command.c
Added code for selecting atom areas with mouse: changed
PickAtom() function name in PickAtoms(); changed PicAtome
identifier in PickAtom; added function SelectArea()
and DisplayArea(); added code for command "select view"
[30/01/00] PV command.c
Added command "select view" and corresponding code,
which allows to select a part of a molecule based on screen display.
[16/01/00] PV cmndline.c
In PerformMouseFunc() corrected MM_CLIP to access clipping with
the mouse, added MM_DEPT to access backclipping (depth) with the mouse.
[16/01/00] PV transfor.h, transfor.c, token.h, token.c, script.c
Added ShadePower in DefineColourMap(), which brings some interesting
shade variations. Added ShadePowerTok and command "set shade x"
with x between -20 to 20.
[03/01/00] PV transfor.c
Fixed bug (and modified) function Power() to handle Specpower
[12/14/99] PV
Added variables ShiftS and UseAutoDepthCue that adjust DepthCue
with slabbing.
[14/12/99] PV transform.c
Added function CentreTransform() to either move the origin in the
molecule or move the molecule to the origin (origin = True ).
Added variables Cenx,y,z, which mesure distance centre-origin.
[29/09/99] PV molecule.c
Fixed bug in FindCisBonds() (no zeroing of last group cisbondflag);
Added ability to convert triple bond to single (CreateBondOrder())
[24/09/99] PV cmndline.c
Correlated mouse binding to global variable MouseMode.
Removed EnableMenus(state==1) in ResetCommandLine().
Fixed mouse binding with INVERT on y values.
Fixed bug on capture status on mouse-up. Added MM_PREV
to mouse binding for deselection. Fixed INVERT on y
value for mouseup.
[21/09/99] PV command.c, render.h, render.c, transfor.h, transfor.c
Added four new picking modes: select an atom: PickAtom; select
a group: PickGroup; select a chain: PickChain; modify bonding/add
multiple bonds: PickBond. Allowed picking parameter shift = -1
when Ctrl key is down to deselect an atom (a group, a chain)
from the current selection. [Note by HJB 02/04/01 -- The UCB
and 2.7.2 bond picking was used in 2.7.2.1 instead of the
RasTop version]
[22/09/99] PV abstree.h, abstree.c
First step for saving atomsets & identifiers in RasMol scripts
(SetSize to 100 and SymEntry and SymbolTable in header).
[21/09/99] PV cif.h
Fixed missing declaration of cif_parse in cif.h
[21/09/99] PV cmndline.c
In ProcessCharacter()) added ESC (0x1b) character to interrupt
script pausing.
[21/09/99] PV command.c
Changed output for one-letter-code sequence in series of 50
characters with a space each subgroup of 10.
[21/09/99] PV infile.c
Compiling problems with RasMol 2.7.1 files (VisualC++ 5.0)
- explicited all conversions long to short in infile.c /*casting*/
[21/09/99] PV pixutils.c
Compiling problems with RasMol 2.7.1 files (VisualC++ 5.0)
- fixed casting in drawstar() and clipstar() in pixutils.c
Set ARCSIZE to 32768 under MSWIN, allowing drawing cylinders with
radii up to 250 RasMol Units. Current implementation gives a maximum
of 75 RU at maximum zooming. Mac implementation should be verified.
[14/07/99] PV abstree.c transfor.c
(Adapted from RasTop 1.3) Added shortcuts for direct evaluations
of atomsets (BuildAtomSet(), SelectZoneExpr()).
[14/07/99] PV abstree.c, transfor.c
Added shortcuts for direct evaluations of atomsets (BuildAtomSet(),
SelectZoneExpr()); gain up to 15 seconds of computer time on very
large molecules.
[10/07/99] PV cif.c
Fixed memory allocation bug in cif_make_handle
Changes from RasMol 2.7.1 to create RasMol 2.7.2:
[28/08/00] HJB all
Updates to comments, resources, etc for preliminary testing
release.
[21/08/00] HJB abstree.c, abstree.h
Change type Atom to RAtom to avoid conflicts with X.
Offset all uses of xorg, yorg, zorg databse entried with
fxorg, fyorg, fzorg database entries for UCB bond
rotation. Change char* strings to unsigned char* strings
to allow for extra UCB Angstrom and degree symbols.
[21/08/00] HJB applemac.c
Change from use of toolbar settings to use of RotMode.
Add new "Settings" menu.
[21/08/00] HJB cmndline.c
Adapt GSG code from UCB mods for mouse moves, to make
the moves control bond rotation, molecule rotation, or
world rotation, but change from use of toolbar settings
to use of RotMode
[21/08/00] HJB command.c
Add new error message (ErrNoBond) for "Bond for rotation
not picked". Add new parameter for alternate conformer
bond waist radius. Adapt to fxorg, etc. offsets. Adapt
GSG UCB pick bond tool bar button to a command line
command. Add show centre, show rotation, show translation
and show zoom commands. Add bond, unbond commands.
Add rotate bond, rotate molecule, rotate all command.
[21/08/00] HJB command.h
Add space after "__huge"
[21/08/00] HJB font.h
Adapt GSG UCB mods characters for Angstrom and degree to be
additional symbols, not repalcements.
[21/08/00] HJB graphics.h
Add new redraw flag, "RFRotBond" to signal that a bond
rotation is involved, and add it to RFRotate, RFApply and
RFInitial. Add ZRange. Move main X window definitions
into this header to facilitate toolbar development.
[21/08/00] HJB infile.c, infile.h
Change all Atom types to RAtom. Add xorg, etc. offsets
on all coordinate calauclations. Move GroupPool definition
to header.
[21/08/00] HJB molecule.h and all referring files
Change type Atom to RAtom to avoid conflicts with X.
Add fxorg, fyorg, fzorg database entries for UCB bond
rotation offsets.
[21/08/00] HJB multiple.c
Remove all use of the toolbar, converting to menu.
Detect last element of file name string. Update VarList
for current variables. Change to ANSI C prototypes.
Move revised DrawMoleculeList from GSG's UCB toolbar.c
into multiple.c, but drop list only into MolName[].
[21/08/00] HJB wbrotate.c, wbrotate.h
Remove all use of the toolbar, converting to menu.
Change to ANSI C prototypes. Revise bond and world
rotation logic to use full rotation, nor increment,
for improved accuracy. Change Bond rotation logic to
preserve nesting of bonds without changing the original
coordinates. Add database of selected bonds and logic
to add bonds on the fly and remove them.
[21/08/00] HJB vector.c, vector.h
Change to ANSI C prototypes. Replace Vector and Matrix
with their array definitions for clarity.
[27/02/00] HJB transfor.c, transfor.h
Add alternate conformer bond radius to EnableWireFrame
[23/02/00] HJB infile.c
Fix *- for - typo in XYZ and MOL2 input of coordinates
[23/02/00] HJB molecule.c
Fix D2O to DOD mapping. Thanks to Brian W. Beck.
[23/02/00] HJB pixutils.c
New code for alternate conformer bonds.
[23/02/00] HJN raswin.c
Update WinMail entry to WINAPI
[29/01/00] HJB molecule.c
Comment out chain by chain reset of bonding to allow for
het groups after TER at expense of slower bonding.
[29/01/00] HJB mswin31.c
Update printer logic for modern windows specs.
[29/01/00] HJB rasmac.c
Fix reference of monaco font.
[15/07/99] HJB (for AR) raswin.c
Add check for \r. Thanks for Andrew Raine.
[15/07/99] RS raswin.c
Add .ML2 and .SY2 extensions for Sybyl and MOL2.
Changes adapted from UCB rasmol in creating RasMol 2.7.2:
Note: These mods do not reflect the complete source of UCB RasMol. In particular
toolbar.h and toolbar.c have not been used in this pass, and the full source of UCB
RasMol has not yet been recovered.
[30/11/95] GSG rasmac.c
Hide command window. Add help screen menu logic. Add hooks to
load multiple molecules. Add toolbar menu to Windows menu. Make
mouse moves control bond rotation, molecule rotation or world
rotation depending on tool bar button choices. Same for scroll
bars.
[29/11/95] GSG applemac.c
Change default background for printing to white.
Hook scroll bar H values to bond angle (BRotValue),
molecule rotation angle (DialValue[1]) or
world rotation angle (WRotValue[1]) depending on
toolbar settings. Hook scroll bar V values to
molecule rotation angle (DialValue[0]) or
world rotation angle (WRotValue[0]) depending on
tool bar settings. Allow file open when less than
MAX_MOLECULES molecules.
[21/08/00] GSG font.h
Add characters for Angstrom and degree as replacements
for vertical bar and tilde.
[16/11/95] GSG render.c, render.h
Add PickBond. Add hooks to draw multiple molecules. Automatically
switch to the molecule of any picked atom. Add monitor for picked
distance, angle or torsion angle.
[14/11/95] GSG transfor.c
Add hooks for bond rotation and global rotation.
[14/11/95] GSG vector.c, vector.h, wbrotate.c, wbrotate.h
New routines introduced with UCB mods to allow for
bond rotations and global rotation.
[14/11/95] GSG infile.c
Add fxorg, fyorg, fxorg for MDL molecule input only.
[14/11/95] GSG molecule.c, molecule.h
Add fxorg, fyorg, fxorg and list of bonds to atom database
for world and bond rotation.
[11/11/95] GSG multiple.c, multiple.h
New routine introduced with UCB mods to allow for
multiple molecules.
[10/11/95] GSG tokens.c,tokens.h
Add MoleculeTok.
[10/11/95] GSG repres.h
Add flag for units to Monitors.
[09/11/95] GSG command.c, command.h
Add hooks for multiple molecules. Log background
status to allow default white print background.
Add molecule command.
[09/11/95] GSG rasmol.c
Add initialisation for multiple molecules.
Changes from RasMol 2.7.1 to create RasMol 2.7.1.1:
[21/01/01] FGR, HJB langsel.c, langsel_mac.c, mswin.c, applemac.c
Installed translations for Edit menu on mac and PC
provided by Fernando Gabriel Ranea.
[17/01/01] FGR, HJB langsel.c, langsel_mac.c
Corrections to translations by Fernando Gabriel Ranea, installed
by HJB with revisions to menu bar accelerators.
[12/01/01] HJB applemac.c
Added include of langsel.h. Added routine ReWriteStr255 to rewrite
menu bar items in place and tostr255 to convert other menu items
strings to Pascal form for use in SetmenuItemText. Set up
ReDrawWindow to refresh all menu strings and then redraw the menu
bar. Note that the rewrite of the main menu bar is _very_ risky
and may not survive system changes.
[12/01/01] HJB command.c
Added include of langsel.h. Remove redundant ErrorMsg array and Err...
definitions. Change messages to reference MsgStrs. Add English and
Spanish as commands calling SwitchLang.
[12/01/01] HJB infile.c
Fix coordinate typo in load of XYZ and Mol2 molecules.
[12/01/01] HJB langsel.c, langsel_mac.c, langsel.h
New routines to carry multi-lingual translations. Many thanks to
Fernando Gabriel Ranea for the bulk of the Spanish translations,
and for creating the initial Spanish version of RasMol 2.7.1. Note
that langsel.c uses the ANSI character set, while lansel_mac.c uses the
Macintosh character set.
[12/01/01] HJB molecule.c
Added include of langsel.h. Changed messages to reference MsgStrs.
Refixed D2O misparse, which had been previously fixed. Mod had been
lost.
[12/01/01] HJB mswin31.c
Added include of raswin.idm and langsel.h. Included partial update
to printer logic. Added ReDrawWindow as rewrite of menus with
ModifyMenu and RemoveMenu/AppendMenu calls.
[12/01/01] HJB rasmac.c
Added include of langsel.h. Added SwitchLang(English) calls
for initialization to main routine.
[12/01/01] HJB rasmol.c
Add fix for broken math routines by referencing atan2.
[12/01/01] HJB rasmol.h
Added include of langsel.h. Added SwitchLang(English) calls
for initialization to main routine.
[12/01/01] HJB raswin.c
Added include of langsel.h. Changed font of command window to ANSI
character set. Changed most messages to reference MsgStrs. Add
SwitchLang(English) calls for initialization to WinMain.
[12/01/01] HJB x11win.c
Restructured MenuItem and BarItem to make .text, .pos and .len
indirect, so that they can be fetched from MsgStrs, MsgAuxl and
MsgLens. The .pos field is used to specify the character offset
of the acceleration key. The main menu bar may now have non-zero
offsets. All the menu items have been changed to MsgStrs[StrM...]
referecences, and added include of langsel.h. Added ReDrawWindow
simply as a call to ReSizeWindow. This is overkill, but appropriate
for these infrequent calls.
[12/01/01] HJB tokens.h
Added tokens EnglishTok and SpanishTok.
[12/01/01] HJB graphics.h
Added prototype of ReDrawWindow, a system-dependent call to be used
after updating menus on language changes.
[12/01/01] HJB cmndline.c
Added include of langsel.h, changed prompts as follows:
"PDB file name:" MsgStrs[StrPrmtPDB]
"Image file name:" MsgStrs[StrPrmtImg]
"Molecule file name:" MsgStrs[StrPrmtMol]
[12/01/01] HJB tokens.c
Added the following tokens:
CADENA ChainTok
CADENAS ChainTok
DIBUJO CartoonTok
DIBUJOS CartoonTok
E AndTok
EJE AxesTok
EJES AxesTok
ELANCE BondTok
ELANCES BondTok
ENGLISH EnglishTok
ESQUELETO BackboneTok
ETIQUETA LabelTok
ETIQUETAS LabelTok
GIRO TurnTok
GIROS TurnTok
GRUPO GroupTok
HEBRAS StrandsTok
MOSTRAR DisplayTok
SALIR ExitTok
SPANISH SpanishTok
TODO AllTok
[26/12/99] HJB mswin31.c
Do not reset Voxel Data for each chain.
[02/10/99] HJB molecule.c
Update printer logic.
Changes from RasMol 2.7.0 to RasMol 2.7.1.1 include:
* Introduction of a multilingual structure for RasMol.
* Population of messages and menu lists for English and Spanish.
* Upgrade of some of the Windows printer logic
* Correction of coordinate handling for Mol2 and XYZ coordinates
* Fix to the parsing of D2O.
* The ability to automatically mark non bonded atoms in wireframe and stick displays.
Our thanks to R. Curtis Haltiwanger for suggesting this change.
* The ability to use a proportionally spaced font and to draw labels with heavier
strokes. Our thanks to Eric Martz for suggesting this change.
* The ability to auto-recognize PDB vs. CIF and mmCIF datasets.
* Extensive updating to the manual. Our thanks to William McClure, Margaret Wong, Eric
Martz and Frances Bernstein.
* Updating the canvas title with the PDB ID code and EXPDTA information, so models will
be clearly distinguished from experimental data. Our thanks to Helen Berman for
suggesting this change.
* The ability to report coordinates.
* Additions to the list of pre-defined colours.
* Improved accuracy of coordinates in pseudo-PDB output.
* Fixes to the centering logic.
Changes from RasMol 2.7.0.1 to create RasMol 2.7.1:
[15/07/99] HJB documentation
Add Dunix binaries. Thanks to David Atkinson
[06/07/99] HJB all
Release 2.7.1
[05/07/99] HJB documentation
Cut-off date for Release 2.7.1 documentation changes.
[22/06/99] HJB all source
Cut-off date for Release 2.7.1 code changes.
[22/06/99] HJB command.c
Save fact that a data file was loaded inline. Add
processing for star command, all new options for
bondmode [all | none | not bonded ]
[22/06/99] HJB infile.c
Update DataFileFormat after autorecognition.
[22/06/99] HJB molecule.h
Add MarkAtoms to hold new bondmode flags.
[22/06/99] HJB pixutils.c, render.c
Add code for new star command.
[22/06/99] HJB script.c
Add logic to write star command output. Report data
loaded as CIF or as inline correctly. Warn users
that inline data is not being written out. Check
inversion of Y-axis on POVRAY3. Thanks to Curt
Haltiwanger for suggesting marking non-bonded atoms
on wireframe displays.
[22/06/99] HJB transfor.c
Add code for new star command, new bondmode options.
[18/06/99] HJB pixutils.h, pixutils.c
Change name of DisplayString to DisplayRasString to
avoid a conflict with X libraries. Add FontWid array
to hold character widths (FontSize for FS, FontSize/4
+1 + maximum x position for PS). Add FontStroke logic to
write cylinders instead of lines when FontStroke is not
zero.
[18/06/99] HJB render.c
Change name of DisplayString to DisplayRasString to
avoid a conflict with X libraries.
[18/06/99] HJB repres.c
When FonstStroke is non-zero, don't offset character
color by (ColourMask>>1), to allow room for color
adjustments in cylinder drawing.
[18/06/99] HJB script.c
Add logic to write PS flag for proportional spacing
on set fontsize, and logic to write set fontstroke n.
[18/06/99] HJB tokens.c, tokens.h
Add tokens for BlueTint (BlueTintTok), Brown (BrownTok),
FontStroke (FontStrokeTok), FS (FSTok), Gold (GoldTok),
Gray or Grey (GrayTok), GreenTint (GreenTintTok), HotPink
(HotPinkTok), Pick as an alternative for Picking
(PickingTok), Pink (PinkTok), PinkTint (PinktintTok),
SeaGreen (SeaGreenTok), SkyBlue (SlyBlueTok),
YellowTint (YellowTintTok)
[13/06/99] HJB command.c
Change processing of load inline command to work from
the currently opened script, saving the file position.
Accept HEADER and DATA_... as commands in a script,
processing that line and all subsequent lines as a
data file, unless a prior load inline command was already
done
[12/06/99] HJB infile.c
When processing a PDB file, test for DATA_... until
a non-comment, non-blank line is found. Revert
to CIF processing if DATA_... is found.
[11/06/99] HJB infile.c
In PDB format input extract EXPDTA for Info.technique.
In CIF format input accept _audit_block_code for the
entry ID, _exptl.method, _diffrn_radiation.probe or
_diffrn_radiation_probe for Info.technique. Preserve
low order bits of coordinates in xtrl, yrtl, ztrl. On
PDB output, report Info.technique in EXPDTA and reinsert
low-order bits for coordinates.
[10/06/99] HJB abstree.c
Add code to report coordinates for show selected cordinates
[10/06/99] HJB command.c
Recognize new commands, picking coordinates,
show selected cordinates. Update default title produced
by title command.
[10/06/99] HJB molecule.h
Add new Info fields for date and technique. Extend
identcode to 80 columns. Add CRD to Selection enum type.
Add prototype for ReviseTitle.
[10/06/99] HJB render.h, render.c
Add code to report coordinates for picking coordinates,
define PickCoord symbol.
[10/06/99] HJB tokens.h, tokens.c
Add code recognize COORD, COORDS, COORDINATE, COORDINATES for
new CoordTok, DATA_... for CIFDataTok, HEADER for HeaderTok
[09/06/99] HJB molecule.c
Put PDB entry ID and EXPDTA info into canvas title, report
EXPDTA data from Info.technique on reading file.
[06/06/99] HJB infile.c
Restore the origin on PDB and other outputs.
[06/06/99] HJB script.c
Change script output to include centering and
change various coordinate outputs to restore
origins the z-axis orientation.
[06/06/99] HJB command.c
Add command centre [CenX,CenY,CenZ] to center by offsets
from centre of gravity.
[03/06/99] HJB render.c
Remove call to TranslateToCentre, hold centering
in CenX, CenY and CenZ, decoupled from dials,
add RFRotate to ReDrawFlag on centering. Thanks to
Bohdan Schneider for pointing out the problems with
centering.
[03/06/99] HJB transfor.c
Remove TranslateToCentre, remove processing of CenX,
CenY and CenZ from dial values, and put it into
computation of ptr->x,y,z
Changes after release of RasMol_2.7.0.1:
[27/04/99] HJB README.html, Changelog.html, INSTALL.html, manual
Add navigation links at top and bottom of each page.
Add links for gzipped versions of raswin.hlp, rasmol.hlp.
Thanks to E. Martz and Kjeld Olesen.
[27/04/99] HJB INSTALL.html, manual
Replace empty copy of INSTALL.html in doc/, correct
embedded html in manual. Thanks to Kurt Giles.
Changes from RasMol_2.7.0 to create RasMol_2.7.0.1:
[22/04/99] HJB
Announce RasMol 2.7.0.1 on pdb-l@rcsb.org,
rasmol@lists.umass.edu, mmciflist@ndbdev.rutgers.edu
[11/04/99] HJB *.c, *.h
Update all comment blocks for new version and date
[11/04/99] HJB abstree.h
Realign Pred... to agree with ...Tok to correct
misaligned introduced by HJB (not AM) during merge of 2.6x1
into 2.7.0.
[11/04/99] HJB tokens.h
Fix definition of IsPredTok
[09/04/99] HJB molecule,h
Make residue identification case-insensitive.
Changes from RasMol_2.6.4, RasMol2.6x1 and RasMol_2.6_CIF.2 to create RasMol_2.7.0:
[30/03/99] HJB all
Cleanup and release of version 2.7.0
[23/03/99] HJB abstree.c
Add code to select on alternate conformers. Increase
accuracy of torsion angle calculation.
[23/03/99] HJB command.c, command.h
Make InitHelpFile generally available, change to
WriteString for reporting CisBondCutOff for use on mac,
report models on show selected.
[23/03/99] HJB rasmol.c, raswin.c, rasmac.c
Add suggestion for help notice to initial text lines.
[23/03/99] HJB script.c
In order to support mac introduce WriteBuffer and
change all fprintf(outFile, ... to WriteBuffer, provide
code from fisipl for Ramachandran printer plot. Handle
signs of torsion angles. Thanks to F. C. Bernstein.
[23/03/99] HJB tokens.h, tokens.c
Add RamPrintTok, RPP, RDF, etc., hook POVRAY3 to the
new POVray code.
[20/03/99] HJB *.h, *.c
In general, the RasMol_2.6_CIF.2 version was used as a base
and upgraded with the RasMol_2.6.4 changes. The exceptions
are below
[20/03/99] HJB infile.c
Cell parameters are read with the double routine ReadDecValue
from 2.6_CIF.2, rather than ReadValue2 from 2.6.4
Changes from RasMol_2.6 to create RasMol_2.6x1:
[15/2/98] AM abstree.c, abstree.h
Add PredCisBond, DescribeObj, CalcPhiAngle, CalcPsiAngle,
CalcOmegaAngle, shift torsion angle calculations 180
degrees.
[15/2/98] AM command.c
Add FindCisBonds, CisBondCutOff, show of selected chains,
groups, atoms, show and write of phi-psi angles
[15/2/98] AM molecule.h, molecule.c
Add CIS bond logic
[15/2/98] AM rasmol.h, rasmol.c
Add USE_FD_SET_TYPE option
[15/2/98] AM script.h, script.c
Add WritePhiPsiAngles, code for POV-Ray version 3
[15/2/98] AM tokens.h
Add CisBondedTok, RamachanTok, CisAngleTok, PhiPsiTok,
define PHIPSI, CISANGLE, RAMACHAN, CISBONDED
Changes from RasMol_2.6 to create RasMol_2.6.4:
[8/2/99] RS command.c, rasmol.c, scripts.c, rastxt.c, raswin.c
rasmac.c
Final fixup and release of version 2.6.4
[27/12/98] RS *.h, *.c
Remove all non-ANSI-C prototypes and ensure use of ( void )
for empty argument lists. Upgrade all procedure delcarations.
Convert to use of MSWIN.
[27/12/98] RS abstree.c
Redo torsion angel calculation.
[27/12/98] RS applemac.c
Convert to Apple's new routine names
[27/12/98] RS cmndline.c, cmndline.h
New routine for mouse, keyboard, dials
[27/12/98] RS command.c, command.h
Move routines for mouse, keyboard, dials to cmndline.c.
Redo ParseColour. Reorganize command parsing
[27/12/98] RS infile.c
Change references to MMIO to MMIOLIB. Pass fp and buffer
to FetchRecord as argument. Add ReadValue2, ProcessPDBBond,
ProcessPDBUnitCell. Fix recognition of END. Use
InvalidateCmndline and UnusedArgument. Write MODEL and
ENDMDL records when appropriate
[27/12/98] RS molecule.c
Reorganize FindResNo as a character-oriented search tree
Add Cache.
[27/12/98] RS rasmac.c
Convert to Apple's new routine names
[27/12/98] RS rastxt.c
New text-only main program
[27/12/98] RS repres.c
Add LabelTermnii
[27/12/98] RS tranfor.c
Add TranslateToCentre
[27/12/98] RS transfor.h
Reorganize the logic defining DefaultAmbient, making
the default value 0.4 instead of 0.6, except for E&S, which
is still .05.
[27/12/98] RS tokens.c
New routine for character-oriented search tree for tokens.
[01/08/97] RS infile.c
Decreased the maximum valid alpha carbon to alpha carbon
distance to 4.2 Angstroms from 7.0 Angstroms. Thanks to
Kostas Sfyrakis and Harren Jhoti.
[15/04/97] RS molecule.c repres.c
Fixed a bizarre feature in the OpenVMS compiler that complained
about "a=*b" as "=*" operator is an obsoltete form and may not
be portable. Special thanks to Remington Stone.
[28/11/96] RS rasmol.h rasmol.c
Several minor fixes to compile RasMol under VMS. Special
thanks to Adam Ralph (and CCP4).
Changes from RasMol_2.6_CIF(Rev 1) to create RasMol_2.6_CIF(Rev 2):
[24/2/99] HJB Release of RasMol_2.6_CIF(Rev 2) at
http://www/bernstein-plus-sons.com/software/rasmol
and announce to mailing lists.
[21/2/99] HJB cif.h
Add prototypes of cif_make_handle, cif_read_file,
cif_make_file, cif_save_character to avoid compiler warnings
[21/2/99] HJB cif_ctonum.c
Remove unneeded values.h
[21/2/99] HJB cif_ctonum.h
Correct prototype
[21/2/99] HJB infile.c
Add cif_ctonum.h, define LoadCIFMolecule prototype,
initialize ch, add return to avoid compiler warnings.
[21/2/99] HJB abstree.c, cif.c, cif_ctonum.c, command.c,
infile.c, molecule.c
Use string_case.h instead of for IBMPC,
VMS and APPLEMAC.
[21/2/99] HJB rasmol.h
Update version, add some definitions from R. Sayle's
2.6.4 in preparation for 2.7.0.
[21/2/99] HJB rasmac.c, rasmol.c, raswin.c
Update reported date on startup.
[21/2/99] HJB render.c
Add cif_fract.h to avoid compiler warnings.
[21/2/99] HJB string_case.c
Replace garbled version, provide string_case.h.
[21/2/99] HJB script.c
Initialize first, last, radius, to avoid compiler warnings
[21/2/99] HJB transfor.c
Initialize min and max to avoid compiler warnings.
[10/1/99] HJB Release of RasMol_2.6_CIF(Rev 1) at
http://www.bernstein-plus-sons.com/software/rasmol
and announce to mmCIF mailing list.
[9/1/99] HJB cif.c
Change toupper calls to ToUpper calls.
[8/1/99] HJB command.c
Add argument to CreateMoleculeBonds to force zapping
on connect.
[8/1/99] HJB infile.c
Log requested bonds which cannot be made in NullBonds
and report to users, add RightJustify to right-justify
residue names, recognize _atom_site_disorder_group
for small molecule alternate conformerse, recognize bonds
which don't have either atom names or atom numbers.
[8/1/99] HJB molecule.c
Add argument to CreateMoleculeBonds to force zapping
on connect.
[8/1/99] HJB molecule.h
Add argument to CreateMoleculeBonds to force zapping
on connect, add NullBonds to log requested bonds which
cannot be made.
[8/1/99] HJB mswin31.c
Use VERSION to construct window title.
[8/1/99] HJB outfile.c
Use VERSION to construct Postscript output file header.
[8/1/99] HJB rasmac.c
Use VERSION to report version on startup.
[8/1/99] HJB rasmol.c
Use VERSION to report version on startup.
[8/1/99] HJB raswin.c
Use VERSION to report version on startup.
[8/1/99] HJB script.c
Use VERSION to construct various output file headers.
[8/1/99] HJB x11win.c
Use VERSION to construct window title.
Changes from RasMol_2.6 to create RasMol_2.6_CIF:
[22/12/98] HJB Preliminary release of RasMol_2.6_CIF at
http://www.bernstein-plus-sons.com/software/rasmol
[19/12/98] HJB command.c
correct handling of internal help files under windows,
and allow for unix help files on a mac.
[18/12/98] HJB Makefile.in, Imakefile
Update for CIF support.
[09/12/98] HJB infile.c
Cummulative changes for fractional coordinates,
CIF.
[09/12/98] HJB command.c
Changes for alt, model labels, colour schemes,
CIF.
[09/12/98] HJB molecule.h
Cummulative changes for fractional coordinates,
new colour schemes, CIF.
[09/12/98] HJB molecule.c
Cummulative changes for fractional coordinates,
new colour schemes, CIF.
[09/12/98] HJB x11win.c
Update comments, menus and version text.
[09/12/98] HJB mswin31.c
Update comments, output file commentary.
[09/12/98] HJB outfile.c
Update comments, output file commentary.
[09/12/98] HJB script.c
Update comments, output file commentary.
[09/12/98] HJB rasmol.c
Update comments, output file commentary.
[04/12/98] HJB pixutils.c
Update comments, code to stripe bonds for alternate
conformers.
[04/12/98] HJB pixutils.h
Update comments, protytpes to stripe bonds for alternate
conformers.
[04/12/98] HJB rasmac.c
Update comments, adjust code for current Metrowerks
compiler.
[04/12/98] HJB raswin.c
Update comments, adjust code for current Metrowerks
compiler.
[04/12/98] HJB tokens.h
Update comments, tokens for alt, model colours.
[04/12/98] HJB transfor.c
Update comments, add code for alt, model colours.
[04/12/98] HJB transfor.h
Update comments, prototypes for alt, model colours.
[23/11/98] HJB abstree.c
Add code for %A, %M specifiers, divide u/l case.
[22/11/98] HJB cif_fract.c
New routine, derived from cif2pdb by H.J. Bernstein
and F. C. Bernstein.
[22/11/98] HJB cif_fract.h.
New header for cif_fact.c.
[22/11/98] HJB cif_stx.c
New routine, derived from P. Ellis CBFlib parser.
[23/11/98] HJB render.c
Update comments, add code to stripe bonds for alternate
conformers.
[23/11/98] HJB repres.c
Update comments, add code to stripe bonds for alternate
conformers.
[09/09/98] HJB cif_ctonum.c
New routine, derived from ciftbx by S. R. Hall
and H. J. Bernstein.
[09/09/98] HJB cif_ctonum.h
New header for cif_ctonum.c.
[18/08/98] HJB cif.h
New header for cif.c, derived from CBFlib by P. Ellis
and H. J. Bernstein.
[18/08/98] HJB cif.c
New routine derived from CBFlib by P. Ellis and
H. J. Bernstein.
[14/08/98] HJB rasmol.c
Added hooks for termio for Linux. These changes
are similar to, but not identical to the FreeBSD hooks.
See the linux conditionals. -- H. J. Bernstein
Other Changes
The complete version 2 change history is in the directory ChangeLog
-----------------------------------------------------------------------------------------
| OpenRasMol | Copying and Distribution | Contents | Installation Instructions |
| Changes | Things To Do | Introduction | Source Code and Binaries |
| RasMol Manual | Spanish Translation of RasMol Manual | Italian Translation of RasMol Help
File |
| Donate to Support RasMol | Release README | Register your RasMol |
-----------------------------------------------------------------------------------------
Updated 19 July 2009.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com
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the term "modification".) Each licensee is addressed as "you".
Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of
running the Program is not restricted, and the output from the Program
is covered only if its contents constitute a work based on the
Program (independent of having been made by running the Program).
Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's
source code as you receive it, in any medium, provided that you
conspicuously and appropriately publish on each copy an appropriate
copyright notice and disclaimer of warranty; keep intact all the
notices that refer to this License and to the absence of any warranty;
and give any other recipients of the Program a copy of this License
along with the Program.
You may charge a fee for the physical act of transferring a copy, and
you may at your option offer warranty protection in exchange for a fee.
2. You may modify your copy or copies of the Program or any portion
of it, thus forming a work based on the Program, and copy and
distribute such modifications or work under the terms of Section 1
above, provided that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices
stating that you changed the files and the date of any change.
b) You must cause any work that you distribute or publish, that in
whole or in part contains or is derived from the Program or any
part thereof, to be licensed as a whole at no charge to all third
parties under the terms of this License.
c) If the modified program normally reads commands interactively
when run, you must cause it, when started running for such
interactive use in the most ordinary way, to print or display an
announcement including an appropriate copyright notice and a
notice that there is no warranty (or else, saying that you provide
a warranty) and that users may redistribute the program under
these conditions, and telling the user how to view a copy of this
License. (Exception: if the Program itself is interactive but
does not normally print such an announcement, your work based on
the Program is not required to print an announcement.)
These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the Program,
and can be reasonably considered independent and separate works in
themselves, then this License, and its terms, do not apply to those
sections when you distribute them as separate works. But when you
distribute the same sections as part of a whole which is a work based
on the Program, the distribution of the whole must be on the terms of
this License, whose permissions for other licensees extend to the
entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest
your rights to work written entirely by you; rather, the intent is to
exercise the right to control the distribution of derivative or
collective works based on the Program.
In addition, mere aggregation of another work not based on the Program
with the Program (or with a work based on the Program) on a volume of
a storage or distribution medium does not bring the other work under
the scope of this License.
3. You may copy and distribute the Program (or a work based on it,
under Section 2) in object code or executable form under the terms of
Sections 1 and 2 above provided that you also do one of the following:
a) Accompany it with the complete corresponding machine-readable
source code, which must be distributed under the terms of Sections
1 and 2 above on a medium customarily used for software interchange; or,
b) Accompany it with a written offer, valid for at least three
years, to give any third party, for a charge no more than your
cost of physically performing source distribution, a complete
machine-readable copy of the corresponding source code, to be
distributed under the terms of Sections 1 and 2 above on a medium
customarily used for software interchange; or,
c) Accompany it with the information you received as to the offer
to distribute corresponding source code. (This alternative is
allowed only for noncommercial distribution and only if you
received the program in object code or executable form with such
an offer, in accord with Subsection b above.)
The source code for a work means the preferred form of the work for
making modifications to it. For an executable work, complete source
code means all the source code for all modules it contains, plus any
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anything that is normally distributed (in either source or binary
form) with the major components (compiler, kernel, and so on) of the
operating system on which the executable runs, unless that component
itself accompanies the executable.
If distribution of executable or object code is made by offering
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access to copy the source code from the same place counts as
distribution of the source code, even though third parties are not
compelled to copy the source along with the object code.
4. You may not copy, modify, sublicense, or distribute the Program
except as expressly provided under this License. Any attempt
otherwise to copy, modify, sublicense or distribute the Program is
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However, parties who have received copies, or rights, from you under
this License will not have their licenses terminated so long as such
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5. You are not required to accept this License, since you have not
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Program), you indicate your acceptance of this License to do so, and
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6. Each time you redistribute the Program (or any work based on the
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You are not responsible for enforcing compliance by third parties to
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7. If, as a consequence of a court judgment or allegation of patent
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may not distribute the Program at all. For example, if a patent
license would not permit royalty-free redistribution of the Program by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Program.
If any portion of this section is held invalid or unenforceable under
any particular circumstance, the balance of the section is intended to
apply and the section as a whole is intended to apply in other
circumstances.
It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
integrity of the free software distribution system, which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.
This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.
8. If the distribution and/or use of the Program is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Program under this License
may add an explicit geographical distribution limitation excluding
those countries, so that distribution is permitted only in or among
countries not thus excluded. In such case, this License incorporates
the limitation as if written in the body of this License.
9. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the Program
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either of that version or of any later version published by the Free
Software Foundation. If the Program does not specify a version number of
this License, you may choose any version ever published by the Free Software
Foundation.
10. If you wish to incorporate parts of the Program into other free
programs whose distribution conditions are different, write to the author
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make exceptions for this. Our decision will be guided by the two goals
of preserving the free status of all derivatives of our free software and
of promoting the sharing and reuse of software generally.
NO WARRANTY
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
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WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
Copyright (C)
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Library General
Public License instead of this License.
rasmol-2.7.6.0/INSTALL 0000664 0000000 0000000 00000062036 13364034342 0014223 0 ustar 00root root 0000000 0000000 Installation Instructions
RasMol 2.7.5
Molecular Graphics Visualisation Tool
3 June 2009 (rev. 17 July 2009)
Based on RasMol 2.6 by Roger Sayle
Biomolecular Structures Group, Glaxo Wellcome Research & Development
Stevenage, Hertfordshire, UK
Version 2.6, August 1995, Version 2.6.4, December 1998
Copyright (c) Roger Sayle 1992-1999
and Based on Mods by
+------------------------------------------------------------------------------+
| Author | Version, Date | Copyright |
|-------------------+----------------------+-----------------------------------|
| Arne Mueller | RasMol 2.6x1 May | (c) Arne Mueller 1998 |
| | 1998 | |
|-------------------+----------------------+-----------------------------------|
| Gary Grossman and | RasMol 2.5-ucb | (c) UC Regents/ModularCHEM |
| Marco Molinaro | November 1995 | Consortium 1995, 1996 |
| | RasMol 2.6-ucb | |
| | November 1996 | |
|-------------------+----------------------+-----------------------------------|
| Philippe Valadon | RasTop 1.3 August | (c) Philippe Valadon 2000 |
| | 2000 | |
|-------------------+----------------------+-----------------------------------|
| Herbert J. | RasMol 2.7.0 March | (c) Herbert J. Bernstein |
| Bernstein | 1999 | 1998-2008 |
| | RasMol 2.7.1 June | |
| | 1999 | |
| | RasMol 2.7.1.1 | |
| | January 2001 | |
| | RasMol 2.7.2 August | |
| | 2000 | |
| | RasMol 2.7.2.1 April | |
| | 2001 | |
| | RasMol 2.7.2 August | |
| | 2000 | |
| | RasMol 2.7.2.1 April | |
| | 2001 | |
| | RasMol 2.7.2.1.1 | |
| | January 2004 | |
| | RasMol 2.7.3 | |
| | February 2005 | |
| | RasMol 2.7.3.1 Apr | |
| | 06 | |
| | RasMol 2.7.4 Nov 07 | |
| | RasMol 2.7.4.1 Jan | |
| | 08 | |
| | RasMol 2.7.4.2 Mar | |
| | 08 | |
| | RasMol 2.7.5 June | |
| | 2009 | |
| | RasMol 2.7.5.1 July | |
| | 2009 | |
+------------------------------------------------------------------------------+
RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
and L. Andrews (via the neartree package). Work on RasMol 2.7.5 supported
in part by grant 1R15GM078077-01 from the National Institute of General
Medical Sciences (NIGMS), U.S. National Institutes of Health and by grant
ER63601-1021466-0009501 from the Office of Biological & Environmental
Research (BER), Office of Science, U. S. Department of Energy. RasMol
2.7.4 incorporated changes by G. Todorov, Nan Jia, N. Darakev, P.
Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol 2.7.4 supported
in part by grant 1R15GM078077-01 from the NIGMS/NIH and grant
ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates changes by
Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work on RasMol 2.7.3
supported in part by grants DBI-0203064, DBI-0315281 and EF-0312612 from
the U.S. National Science Foundation and grant DE-FG02-03ER63601 from
BER/DOE. The content is solely the responsibility of the authors and does
not necessarily represent the official views of the funding organizations.
The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
Teemu Ikonen.
and Incorporating Translations by
+-----------------------------------------------------------------------------+
| Author | Item | Language |
|--------------------------------------+--------------------------+-----------|
| Isabel Servan Martinez, | 2.6 Manual | Spanish |
| Jose Miguel Fernandez Fernandez | | |
|--------------------------------------+--------------------------+-----------|
| Jose Miguel Fernandez Fernandez | 2.7.1 Manual | Spanish |
|--------------------------------------+--------------------------+-----------|
| Fernando Gabriel Ranea | 2.7.1 menus and messages | Spanish |
|--------------------------------------+--------------------------+-----------|
| Jean-Pierre Demailly | 2.7.1 menus and messages | French |
|--------------------------------------+--------------------------+-----------|
| Giuseppe Martini, Giovanni Paolella, | 2.7.1 menus and messages | Italian |
| A. Davassi, M. Masullo, C. Liotto | 2.7.1 help file | |
|--------------------------------------+--------------------------+-----------|
| G. Pozhvanov | 2.7.3 menus and messages | Russian |
|--------------------------------------+--------------------------+-----------|
| G. Todorov | 2.7.3 menus and messages | Bulgarian |
|--------------------------------------+--------------------------+-----------|
| Nan Jia, G. Todorov | 2.7.3 menus and messages | Chinese |
|--------------------------------------+--------------------------+-----------|
| Mamoru Yamanishi, Katajima Hajime | 2.7.3 menus and messages | Japanese |
+-----------------------------------------------------------------------------+
This Release by
Herbert J. Bernstein, Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
yaya@bernstein-plus-sons.com
Copyright (c) Herbert J. Bernstein 1998-2009
The original RasMol manual was created by Roger Sayle. In July 1996, Dr.
Margaret Wong of the Chemistry Department, Swinburne University of
Technology, Australia, made extensive revisions to the RasMol 2.5 manual
to accurately reflect the operation of RasMol 2.6. Eric Martz of the
University of Massachusetts made further revisions. In May 1997, William
McClure of Carnegie Mellon University reorganized the HTML version of the
manual into multiple sections which could be downloaded quickly and added
use of frames. Portions of the 2.7.1 version of the RasMol manual were
derived with permission from William McClure's version using Roger Sayle's
rasmol.doc for version 2.6.4 as the primary source. Changes were made in
August 2000 for RasMol version 2.7.2, January 2001 for RasMol version
2.7.1.1 and April 2001 for RasMol version 2.7.2.1 and February 2005 for
RasMol version 2.7.3.
Documentation Last Updated 19 July 2009
Edited by Herbert J. Bernstein and Frances C. Bernstein
Translations
Thanks to the efforts of Jose Miguel Fernandez Fernandez (Departamento de
Bioquimica y Biologia Molecular. Universidad de Granada. Espana
(jmfernan@ugr.es)) a translation of the Manual for Rasmol version 2.7.1
into Spanish is now available. La traduccion espanola del manual de la
version de la Dra. Wong revisada por Eric Martz fue realizada por Isabel
Servan Martinez y Jose Miguel Fernandez Fernandez. La actual traduccion
del Manual de RasMol 2.7.1 ha sido realizada usando como base la anterior
de RasMol 2.6 por Jose Miguel Fernandez Fernandez.
Thanks to translations by Fernando Gabriel Ranea
in late 2000 and early 2001, RasMol is now capable of rendering most menu
items and messages in Spanish. Jean-Pierre Demailly
provided French translations of
menus and messages in January 2001. Giuseppe Martini
and Giovanni Paolella
with contributions by A. Davassi, M. Masullo and C. Liotto provided
Italian translation of menus and messages in March 2001.
----------------------------------------------------------------------
THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS
***** USE WITH CAUTION ******
----------------------------------------------------------------------
IMPORTANT - Copying and Distribution
This version is based directly on RasMol version 2.7.4.2, on RasMol
version 2.7.4.1, on RasMol version 2.7.4, on RasMol version 2.7.3.1, on
RasMol vesion 2.7.3, on RasMol version 2.7.2.1.1, on RasMol version 2.7.2,
on RasMol version 2.7.1, on RasMol version 2.6_CIF.2, on RasMol version
2.6x1, on RasMol version 2.6.4, and RasMol 2.5-ucb and 2.6-ucb.
Please read the file NOTICE for important notices which apply to this
package and for license terms (GPL or RASLIC).
----------------------------------------------------------------------
Obtaining RasMol v2.7.5
In order to install RasMol, you may start with a compiled binary or work
from the source code.
The complete source code and user documentation of RasMol 2.7.5 may be
obtained from http://blondie.dowling.edu/projects/rasmol and
http://blondie.dowling.edu/projects/rasmol. and by anonymous FTP at:
ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.5.tar.gz
or on the web at:
http://www.bernstein-plus-sons.com/software/RasMol_2.7.5.tar.gz
As compiled version become available, they will be posted at
http://blondie.dowling.edu/projects/rasmol and
http://blondie.dowling.edu/projects/rasmol.
To transfer by anonymous ftp, type "ftp ftp.bernstein-plus-sons.com" on
the command line. Several seconds later you'll be prompted for a username.
Use the username "anonymous" and when asked for a password enter your
e-mail address. Once logged in, type the command "cd software/rasmol" to
change the directory to /software/rasmol and then type "binary" to avoid
corrupting the files during the transfer. For each file you wish to
transfer, type "get " and when you've finished type "quit". If
these files are subsequently transfered to other machines, please remember
to transfer them in BINARY mode. The file sizes should be identical before
and after the transfer.
NOTE: The Mac uses the "carriage return" character to signify the end of a
line, while UNIX machines use a "linefeed". If a file is transfered
between these two machines in "ASCII" mode all such characters are
exchanged, thereby corrupting the archive. Please ensure that you type the
FTP command "binary" before you transfer the file, indicating that the
file should be transfered without translation.
If you wish to start from source code, you will need a RasMol source kit,
and you may need one or more external packages that are not part of
RasMol, but which are used by RasMol.
To build/rebuild RasMol 2.7.5 on any platform, you'll need to transfer the
following file:
RasMol.tar.gz UNIX 'tar'ed 'gzip'ped archive containing the complete
source code and documentation of the RasMol molecular
graphics package.
To unpack the file on a UNIX machine type the command "gunzip
RasMol.tar.gz" and then the command "tar -xvf RasMol.tar" to extract the
files in a subdirectory under the current directory.
*** IMPORTANT CHANGE IN INSTALLATION INSTRUCTIONS FOR RELEASE 2.7.5 ***
You will either need to have the following packages installed in your
system, or to ensure that the indicated defines are at the start
Imakefile:
* http://downloads.sf.net/neartree/NearTree-2.1.3.tar.gz or
#define NEARTREE_LOCAL
* http://downloads.sf.net/cqrlib/CQRlib-1.0.3.tar.gz or
#define CQRLIB_LOCAL
http://http://downloads.sf.net/cvector/CVector-1.0.3.tar.gz or
#define CVECTOR_LOCAL
* http://download.savannah.gnu.org/releases-noredirect/xforms/xforms-1.0.91.tar.gz
or
#define XFORMSLIB_LOCAL
* http://downloads.sf.net/cbflib/CBFlib-0.8.1.tar.gz or
#define CBFLIB_LOCAL
In addition, depending on what has already been installed on your system,
you may need one or more of certain font kits. These packages are not part
of RasMol and normally whould be obtained from their primary web sites,
but, for convenience in installing RasMol, they have been gathered in the
external_packages module in the CVS and as the External_Packages release
on http://blondie.dowling.edu/projects/rasmol and
http://www.sourceforge.net/projects/openrasmol.
These font kits are snapshots of the versions in use at the time of the
build of RasMol 2.7.5. The primary developer web site for each package
should be consulted for the latest versions. Because these kits may not be
the same as later, standard versions that are used by the system, as a
whole, scripts in RasMol that use thses kits (especially font kits) assume
that each kit has been unpacked to a directory _within_ the RasMol build
directory, at the same level as the src directory.
For RasMol release 2.7.5 the package snapshots other than the font kits
have been replaced by the table of downloads listed above.
For building for MS Windows, do not try to use Visual Studio. Use MINGW
instead.
You will need both an appropriate binary and a copy of rasmol.hlp for each
system, and, under Windows, a copy of raswin.hlp for the WinHelp
sub-system.
On an SGI, rename the appropriate binary as rasmol and copy it to
/usr/local/bin/rasmol (or to some appropriate location specified by the
environment variable PATH) and copy rasmol.hlp to
/usr/local/lib/rasmol/rasmol.hlp (or to the location indicated by the
environment variable RASMOLPATH)
----------------------------------------------------------------------
Installing RasMol v2.7.5
UNIX X11:
If you are using a precompiled binary, see the instructions that are
provided with the binary kit. In general, the binary kits for unix
provided directly by this project are tarballs of the
$HOME/lib/RasMol_2_7_5 created by running the script in
src/rasmol_install.sh. The MS windows kit is a NSIS installer to be
double-clicked after downloading.
1. Fonts: Followling the instructions for your system, install whatever
X11 font packages you need to the language variants of RasMol you
intend to use. Almost all Unix variants come with the appropriate
fonts for English, French, Spanish and Italian. There is an
appropriate cyrillic font package, cyr-rfx-windows-1251-1.1, in
external_packages. The Chinese and Japanese fonts in
intlfonts-1.2.1.tar.gz in external_pakages seem to be satisfactory.
2. In the RasMol src directory, either
* Note for 64 bit CPUs: If you are building RasMol for a 64-bit CPU
with a compiler that has a 64-bit long data type, you must either
use the build_all.sh script, or manually
#define _LONGLONG
in rasmol.h
* Modify the #defines in the file rasmol.h (see below) Note: IBMPC
should not be defined.
* either
* Use the script rasmol_build_options.sh to build a new
Imakefile from Imakefile_base. The valid options are:
{--help|-h}
{--cbflib_local}
{--cqrlib_local}
{--cvector_local}
{--neartree_local}
{--xformslib_local}
{--use_xformslib}
{--use_gtk}
{--pixeldepth=32}
{--pixeldepth=16}
{--pixeldepth=8}
{--macosx_fink}
or
* Edit Imakefile to change the desired options by hand. Use of
rasmol_build_options.sh is in general perferred
* either
* execute
&npsp;xmkmf
and
* execute
&npsp;make rasmol
or
* edit the script build_all.sh
* execute build_all.sh
to build as many variants of rasmol as possible.
* A common problem is that SUN OpenWindows keeps its include files
in the directory /usr/openwin/include/X11, hence the compiler
directive -I/usr/openwin/include must be added to CFLAGS.
* A common problem on IBM RS6000s running AIX is that the MIT
shared memory extensions to X windows are in the library
-lXextSam, hence this must be added to the LIBS lines in either
the Makefile or Imakefile.
MS Windows:
If you are using a precompiled binary, follow the instructions
that come with the binary, but in general, you either need to
place raswin.exe, rasmol.hlp and raswin.hlp into the directory
from which you will run, or you need to execute the installer
program by double clicking it.
If you are building from source, you will need MINGW, not visual
studio. CodeWarrior version 9 can also be used.
Macintosh under OSX:
Follow the instructions for unix and run under the X11 system. A
pre-edited version of the build_all.sh script called
build_MACOSX.sh is provided.
COMPILATION DIRECTIVES
The file rasmol.h contains a number of #define directives that
control the runtime behaviour of the program. The following
directives may be defined or undefined to suite the local site.
This determines whether RasMol will display and
THIRTYTWOBIT produce 8bit, 16bit or 32(24) bit output. By default
SIXTEENBIT the symbol EIGHTBIT is defined producing images with
EIGHTBIT up to 256 colours. This symbol must be defined if
IBMPC is defined.
DIALBOX This enables the use of a dials box, that is
connected using the X Window System XInput
extension. This option requires that the program be
compiled with the Xi and Xext libraries. Note: libXi
is called libXinput on some old machines, so
requires the compiler option -lXinput!
MITSHM This option enables the use of the X Window System
MIT shared memory extension. This enables images to
be displayed faster when RasMol and the X11 server
are running on the same host. This option requires
the program be compiled with the Xext library. On
IBM RS6000s runnning AIX, MITSHM also requires the
XextSam library (which requires changing the
Makefile or Imakefile). This is now enabled by
default. This should be disabled on E&S ESV
workstations as MITSHM support is not provided as
standard.
TERMIOS This directive enables the command line processing
on UNIXs that support the termios terminal handling
routines. By leaving this symbol undefined, RasMol
omits the interactive command line interface.
Undefining is not recommended!
SOCKETS This directive enables the TCP/IP server
functionality of RasMol to be enable. This enables
other software to connect to a running RasMol. This
should be undefined on machines not supporting
BSD-style TCP/IP sockets (such as VMS).
APPLEMAC This determines whether the program is to run on an
Apple Macintosh or PowerMac. By default, this option
is disabled. The Macintosh code may be compiled to
be either EIGHTTBIT or THIRTYTWOBIT and will
generate images effectively.
IBMPC This determines whether the program is intended to
run on an IBM PC or compatible. By default, this
option is disabled.
MSWIN This determines whether the program is intended to
run on an IBM PC or compatible under MS Windows. By
default, this option is disabled.
PROFILE Defining PROFILE enables code to profile RasMol
execution.
XPROCARCH Defining XPROCARCH enables code for raswin that gets
detailed information about the operating system and
processor
USE_UNAME Defining USE_UNAME enables code for rasmol under X11
that gets detailed information about the operating
system and processor.
USE_CBFLIB Defining USE_CBFLIB enables code t that depends on
CBFLIB for map reading and writing.
To summarise;
A typical UNIX build:
/* #define IBMPC */
/* #define MSWIN */
/* #define APPLEMAC */
#define X11WIN
#define UNIX
/* #define DIALBOX */
#define SOCKETS
#define TERMIOS
#define PROFILE
#define MITSHM
#define USE_UNAME
#define USE_CBFLIB
A typical Windows build:
#define IBMPC
#define MSWIN
/* #define APPLEMAC */
/* #define X11WIN */
/* #define UNIX */
/* #define DIALBOX */
/* #define SOCKETS */
#define TERMIOS
#define PROFILE
#define MITSHM
#define USE_CBFLIB
A typical Macintosh classic build:
/* #define IBMPC */
/* #define MSWIN */
#define APPLEMAC
/* #define X11WIN */
/* #define UNIX */
/* #define DIALBOX */
#define SOCKETS
#define TERMIOS
#define PROFILE
#define MITSHM
/* #define USE_CBFLIB */
Any comments, suggestions or questions about this modified
version should be directed to Herbert J. Bernstein at
rasmol@bernstein-plus-sons.com.
| OpenRasMol | Copying and Distribution | Contents | Installation Instructions |
| Changes | Things To Do | Introduction | Source Code and Binaries |
| RasMol Manual | Spanish Translation of RasMol Manual | Italian Translation of
RasMol Help File |
| Donate to Support RasMol | Release README | Register your RasMol |
----------------------------------------------------------------------
Updated 19 July 2009.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com
rasmol-2.7.6.0/INSTALL.html 0000775 0000000 0000000 00000061637 13364034342 0015177 0 ustar 00root root 0000000 0000000
RasMol V2.7.5 INSTALL
RasMol 2.7.0 March 1999
RasMol 2.7.1 June 1999 RasMol 2.7.1.1 January 2001
RasMol 2.7.2 August 2000 RasMol 2.7.2.1 April 2001
RasMol 2.7.2 August 2000 RasMol 2.7.2.1 April 2001
RasMol 2.7.2.1.1 January 2004
RasMol 2.7.3 February 2005
RasMol 2.7.3.1 Apr 06
RasMol 2.7.4 Nov 07
RasMol 2.7.4.1 Jan 08
RasMol 2.7.4.2 Mar 08
RasMol 2.7.5 June 2009
RasMol 2.7.5.1 July 2009
RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
and L. Andrews (via the neartree package). Work on RasMol 2.7.5
supported in part by grant 1R15GM078077-01 from the National Institute
of General Medical Sciences (NIGMS), U.S. National Institutes of Health
and by grant ER63601-1021466-0009501 from the Office of Biological &
Environmental Research (BER), Office of Science, U. S. Department of
Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,
N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol
2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and
grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates
changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work
on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281
and EF-0312612 from the U.S. National Science Foundation and grant
DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility
of the authors and does not necessarily represent the official views of
the funding organizations.
The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
Teemu Ikonen.
and Incorporating Translations by
Author
Item
Language
Isabel Serván Martínez,
José Miguel Fernández Fernández
2.6 Manual
Spanish
José Miguel Fernández Fernández
2.7.1 Manual
Spanish
Fernando Gabriel Ranea
2.7.1 menus and messages
Spanish
Jean-Pierre Demailly
2.7.1 menus and messages
French
Giuseppe Martini, Giovanni Paolella, A. Davassi, M. Masullo, C. Liotto
2.7.1 menus and messages
2.7.1 help file
Italian
G. Pozhvanov
2.7.3 menus and messages
Russian
G. Todorov
2.7.3 menus and messages
Bulgarian
Nan Jia, G. Todorov
2.7.3 menus and messages
Chinese
Mamoru Yamanishi, Katajima Hajime
2.7.3 menus and messages
Japanese
This Release by
Herbert J. Bernstein,
Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
The original RasMol manual was created by Roger Sayle. In July 1996,
Dr. Margaret Wong of the Chemistry Department, Swinburne University
of Technology, Australia, made extensive revisions to the RasMol 2.5
manual to accurately reflect the operation of RasMol 2.6. Eric Martz
of the University of Massachusetts made further revisions. In May
1997, William McClure of Carnegie Mellon University reorganized the
HTML version of the manual into multiple sections which could be
downloaded quickly and added use of frames. Portions of the 2.7.1
version of the RasMol manual were derived with permission from
William McClure's version using Roger Sayle's rasmol.doc for
version 2.6.4 as the primary source. Changes were made in
August 2000 for RasMol version 2.7.2, January 2001 for RasMol
version 2.7.1.1 and April 2001 for RasMol version 2.7.2.1 and
February 2005 for RasMol version 2.7.3.
Documentation Last Updated 19 July 2009
Edited by Herbert J. Bernstein and Frances C. Bernstein
Translations
Thanks to the efforts of José Miguel Fernández
Fernández (Departamento
de Bioquímica y Biología Molecular. Universidad de Granada.
España (jmfernan@ugr.es)) a
translation of the
Manual for Rasmol version 2.7.1 into Spanish is now available.
La traducción española del manual de la
versión de la Dra. Wong revisada por Eric Martz fue realizada por
Isabel Serván Martínez y José Miguel Fernández
Fernández. La actual traducción del Manual de RasMol 2.7.1
ha sido realizada usando como base la anterior de RasMol 2.6 por
José Miguel Fernández Fernández.
Thanks to translations by Fernando Gabriel Ranea in late 2000
and early 2001, RasMol is now
capable of rendering most menu items and messages in Spanish.
Jean-Pierre Demailly provided French
translations of menus and messages in January 2001.
Giuseppe Martini and Giovanni Paolella
with contributions by A. Davassi, M. Masullo and C. Liotto provided Italian
translation of menus and messages in March 2001.
THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS
***** USE WITH CAUTION ******
IMPORTANT - Copying and Distribution
This version is based directly on RasMol version 2.7.4.2,
on RasMol version 2.7.4.1,
on RasMol version 2.7.4,
on RasMol version 2.7.3.1,
on RasMol vesion 2.7.3, on RasMol version 2.7.2.1.1,
on RasMol version 2.7.2, on RasMol version 2.7.1, on RasMol
version 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version
2.6.4, and RasMol 2.5-ucb and 2.6-ucb.
Please read the file NOTICE for
important notices which apply to this package and for
license terms (GPL or RASLIC).
Obtaining RasMol v2.7.5
In order to install RasMol, you may start with a compiled binary or work from
the source code.
To transfer by anonymous ftp, type "ftp
ftp.bernstein-plus-sons.com" on the command
line. Several seconds later you'll be prompted for a username. Use the
username "anonymous" and when asked for a password enter your e-mail
address. Once logged in, type the command "cd software/rasmol" to change
the directory to /software/rasmol and then type "binary" to avoid corrupting
the files during the transfer. For each file you wish to transfer, type
"get <filename>" and when you've finished type "quit". If these files
are subsequently transfered to other machines, please remember to
transfer them in BINARY mode. The file sizes should be identical before
and after the transfer.
NOTE: The Mac uses the "carriage return" character to signify the
end of a line, while UNIX machines use a "linefeed". If a file is
transfered between these two machines in "ASCII" mode all such
characters are exchanged, thereby corrupting the archive. Please
ensure that you type the FTP command "binary" before you transfer the
file, indicating that the file should be transfered without
translation.
If you wish to start from source code, you will need a RasMol source kit, and
you may need one or more external packages that are not part of RasMol, but which
are used by RasMol.
To build/rebuild RasMol 2.7.5 on any platform, you'll need to transfer
the following file:
UNIX 'tar'ed 'gzip'ped archive containing the
complete source code and documentation of the
RasMol molecular graphics package.
To unpack the file on a UNIX machine type the command "gunzip
RasMol.tar.gz" and then the command "tar -xvf
RasMol.tar" to extract the files in a subdirectory under the
current directory.
*** IMPORTANT CHANGE IN INSTALLATION INSTRUCTIONS FOR RELEASE 2.7.5 ***
You will either need to have the following packages installed in your system, or
to ensure that the indicated defines are at the start Imakefile:
In addition, depending on what has already been installed on your system,
you may need one or more of certain font kits. These packages are
not part
of RasMol and normally whould be obtained from their primary web sites, but,
for convenience in installing RasMol, they have been gathered in the
external_packages module in the CVS and as the External_Packages release on
http://blondie.dowling.edu/projects/rasmol
and
http://www.sourceforge.net/projects/openrasmol.
These font kits are snapshots of the versions in use at the time
of the build of RasMol 2.7.5. The primary developer web
site for each package should be consulted for the latest
versions. Because these kits may not be the same as later,
standard versions that are used by the system, as a whole,
scripts in RasMol that use thses kits (especially font kits)
assume that each kit has been unpacked to a directory _within_
the RasMol build directory, at the same level as the src
directory.
For RasMol release 2.7.5 the package snapshots other than the font kits have been
replaced by the table
of downloads listed above.
For building for MS Windows, do not try to use Visual Studio. Use MINGW instead.
You will need both an appropriate binary and a copy of rasmol.hlp for each
system, and, under Windows, a copy of raswin.hlp for the WinHelp sub-system.
On an SGI, rename the appropriate binary as rasmol and copy it to
/usr/local/bin/rasmol (or to some appropriate location specified
by the environment variable PATH) and copy rasmol.hlp to
/usr/local/lib/rasmol/rasmol.hlp (or to the location indicated by the
environment variable RASMOLPATH)
Installing RasMol v2.7.5
UNIX X11:
If you are using a precompiled binary, see the instructions that are provided
with the binary kit. In general, the binary kits for unix provided directly
by this project are tarballs of the $HOME/lib/RasMol_2_7_5 created by
running the script in src/rasmol_install.sh. The MS windows kit is
a NSIS installer to be double-clicked after downloading.
Fonts: Followling the instructions for your system, install whatever
X11 font packages you need to the language variants of RasMol you intend to
use. Almost all Unix variants come with the appropriate fonts for English,
French, Spanish and Italian. There is an appropriate cyrillic font package,
cyr-rfx-windows-1251-1.1, in external_packages. The Chinese and Japanese
fonts in intlfonts-1.2.1.tar.gz in external_pakages seem to be satisfactory.
In the RasMol src directory, either
Note for 64 bit CPUs: If you are building RasMol for a 64-bit CPU
with a compiler that has a 64-bit long data type, you must either use
the build_all.sh script, or manually
#define _LONGLONG
in rasmol.h
Modify the #defines in the file rasmol.h (see below)
Note: IBMPC should not be defined.
either
Use the script rasmol_build_options.sh to build a new Imakefile
from Imakefile_base. The valid options are:
{--help|-h}
{--cbflib_local}
{--cqrlib_local}
{--cvector_local}
{--neartree_local}
{--xformslib_local}
{--use_xformslib}
{--use_gtk}
{--pixeldepth=32}
{--pixeldepth=16}
{--pixeldepth=8}
{--macosx_fink}
or
Edit Imakefile to change the desired options by hand. Use of
rasmol_build_options.sh is in general perferred
either
execute
&npsp;xmkmf
and
execute
&npsp;make rasmol
or
edit the script build_all.sh
execute build_all.sh
to build as many variants of rasmol as possible.
A common problem is that SUN OpenWindows keeps its include files in the
directory /usr/openwin/include/X11, hence the compiler directive
-I/usr/openwin/include must be added to CFLAGS.
A common problem on IBM RS6000s running AIX is that the MIT shared
memory extensions to X windows are in the library -lXextSam, hence
this must be added to the LIBS lines in either the Makefile or Imakefile.
MS Windows:
If you are using a precompiled binary, follow the instructions that come
with the binary, but in general, you either need to place raswin.exe,
rasmol.hlp and raswin.hlp into the directory from which you will run,
or you need to execute the installer program by double clicking it.
If you are building from source, you will need MINGW, not visual studio.
CodeWarrior version 9 can also be used.
Macintosh under OSX:
Follow the instructions for unix and run under the X11 system. A pre-edited
version of the build_all.sh script called build_MACOSX.sh is provided.
COMPILATION DIRECTIVES
The file rasmol.h contains a number of #define directives that control
the runtime behaviour of the program. The following directives may be
defined or undefined to suite the local site.
THIRTYTWOBIT
SIXTEENBIT
EIGHTBIT
This determines whether RasMol will display and produce
8bit, 16bit or 32(24) bit output. By default the symbol
EIGHTBIT is defined producing images with up to 256
colours. This symbol must be defined if IBMPC is defined.
DIALBOX
This enables the use of a dials box, that is connected
using the X Window System XInput extension. This option
requires that the program be compiled with the Xi and
Xext libraries. Note: libXi is called libXinput on some old
machines, so requires the compiler option -lXinput!
MITSHM
This option enables the use of the X Window System MIT shared
memory extension. This enables images to be displayed faster
when RasMol and the X11 server are running on the same host.
This option requires the program be compiled with the Xext
library. On IBM RS6000s runnning AIX, MITSHM also requires
the XextSam library (which requires changing the Makefile or
Imakefile). This is now enabled by default. This should be
disabled on E&S ESV workstations as MITSHM support is not
provided as standard.
TERMIOS
This directive enables the command line processing on UNIXs
that support the termios terminal handling routines. By
leaving this symbol undefined, RasMol omits the interactive
command line interface. Undefining is not recommended!
SOCKETS
This directive enables the TCP/IP server functionality of
RasMol to be enable. This enables other software to connect
to a running RasMol. This should be undefined on machines
not supporting BSD-style TCP/IP sockets (such as VMS).
APPLEMAC
This determines whether the program is to run on an Apple
Macintosh or PowerMac. By default, this option is disabled.
The Macintosh code may be compiled to be either EIGHTTBIT
or THIRTYTWOBIT and will generate images effectively.
IBMPC
This determines whether the program is intended to run on an IBM PC or compatible. By default, this
option is disabled.
MSWIN
This determines whether the program is intended to run on an
IBM PC or compatible under MS Windows. By default, this
option is disabled.
PROFILE
Defining PROFILE enables code to
profile RasMol execution.
XPROCARCH
Defining XPROCARCH enables code
for raswin that gets detailed information about the operating system
and processor
USE_UNAME
Defining USE_UNAME enables code
for rasmol under X11 that gets detailed information about the operating system
and processor.
USE_CBFLIB
Defining USE_CBFLIB enables code t
that depends on CBFLIB for map reading and writing.
Updated 19 July 2009.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
rasmol-2.7.6.0/NOTICE 0000775 0000000 0000000 00000075100 13364034342 0014075 0 ustar 00root root 0000000 0000000 COPYING
This version is based directly on RasMol version 2.7.3. This version is
based in large part on RasMol version 2.7.2.1.1, Rasmol version 2.7.2,
RasMol version 2.7.1.1 and RasTop version 1.3 and indirectly on the RasMol
2.5-ucb and 2.6-ucb versions and version 2.6_CIF.2, RasMol 2.6x1 and
RasMol_2.6.4.
RasMol versions 2.7.3 and higher may be distributed under the terms of the
GNU General Public License (the GPL), see
http://www.gnu.org/licenses/gpl.txt
or see below or type the command help GPL in RasMol
or RasMol 2.7.3 may be distributed under the RASMOL license. See the below
or type the command help RASLIC in RasMol
----------------------------------------------------------------------
NEW RasMol Licence (GPL)
(Valid for versions of RasMol starting with Release 2.7.3)
========================== GPL STARTS HERE =================================
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. This
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When we speak of free software, we are referring to freedom, not
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To protect your rights, we need to make restrictions that forbid
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For example, if you distribute copies of such a program, whether
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The precise terms and conditions for copying, distribution and
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0. This License applies to any program or other work which contains
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otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot
distribute so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you
may not distribute the Program at all. For example, if a patent
license would not permit royalty-free redistribution of the Program by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Program.
If any portion of this section is held invalid or unenforceable under
any particular circumstance, the balance of the section is intended to
apply and the section as a whole is intended to apply in other
circumstances.
It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
integrity of the free software distribution system, which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.
This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.
.
8. If the distribution and/or use of the Program is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Program under this License
may add an explicit geographical distribution limitation excluding
those countries, so that distribution is permitted only in or among
countries not thus excluded. In such case, this License incorporates
the limitation as if written in the body of this License.
9. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the Program
specifies a version number of this License which applies to it and "any
later version", you have the option of following the terms and conditions
either of that version or of any later version published by the Free
Software Foundation. If the Program does not specify a version number of
this License, you may choose any version ever published by the Free Software
Foundation.
10. If you wish to incorporate parts of the Program into other free
programs whose distribution conditions are different, write to the author
to ask for permission. For software which is copyrighted by the Free
Software Foundation, write to the Free Software Foundation; we sometimes
make exceptions for this. Our decision will be guided by the two goals
of preserving the free status of all derivatives of our free software and
of promoting the sharing and reuse of software generally.
NO WARRANTY
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
REPAIR OR CORRECTION.
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
.
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
Copyright (C)
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Library General
Public License instead of this License.
=========================== GPL ENDS HERE ==================================
OLD RasMol License (RASLIC)
(Valid for versions of RasMol in the 2.7 series)
========================= RASLIC STARTS HERE ===============================
If you do not use the GPL, the following license terms apply:
RasMol License
Even though the authors of the various documents and software found here
have made a good faith effort to ensure that the documents are correct and
that the software performs according to its documentation, and we would
greatly appreciate hearing of any problems you may encounter, the programs
and documents any files created by the programs are provided **AS IS**
without any warranty as to correctness, merchantability or fitness for any
particular or general use.
THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR
DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS
LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND
NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS.
Subject to your acceptance of the conditions stated above, and your respect
for the terms and conditions stated in the notices below, if you are not
going to make any modifications or create derived works, you are given
permission to freely copy and distribute this package, provided you do the
following:
* 1. Either include the complete documentation, especially the file
NOTICE, with what you distribute or provide a clear indication where
people can get a copy of the documentation; and
* 2. Give credit where credit is due citing the version and original
authors properly; and
* 3. Do not give anyone the impression that the original authors are
providing a warranty of any kind.
In addition, you may also modify this package and create derived works
provided you do the following:
* 4. Explain in your documentation how what you did differs from this
version of RasMol; and
* 5. Make your modified source code available.
========================== RASLIC ENDS HERE ================================
General Notice
Creative endeavors depend on the lively exchange of ideas. There are laws
and customs which establish rights and responsibilities for authors and
the users of what authors create. This notice is not intended to prevent
you from using the software and documents in this package, but to ensure
that there are no misunderstandings about terms and conditions of such
use.
Please read the following notice carefully. If you do not understand any
portion of this notice, please seek appropriate professional legal advice
before making use of the software and documents included in this software
package. In addition to whatever other steps you may be obliged to take to
respect the intellectual property rights of the various parties involved,
if you do make use of the software and documents in this package, please
give credit where credit is due by citing this package, its authors and
the URL or other source from which you obtained it, or equivalent primary
references in the literature with the same authors.
Some of the software and documents included within this software package
are the intellectual property of various parties, and placement in this
package does not in any way imply that any such rights have in any way
been waived or diminished.
With respect to any software or documents for which a copyright exists,
ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT.
Even though the authors of the various documents and software found here
have made a good faith effort to ensure that the documents are correct and
that the software performs according to its documentation, and we would
greatly appreciate hearing of any problems you may encounter, the programs
and documents any files created by the programs are provided **AS IS**
without any warranty as to correctness, merchantability or fitness for any
particular or general use.
THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS
OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR
DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE
OR FILES AND NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS.
----------------------------------------------------------------------
RasMol 2.6 Notice
Information in this document is subject to change without notice and does
not represent a commitment on the part of the supplier. This package is
sold/distributed subject to the condition that it shall not, by way of
trade or otherwise, be lent, re-sold, hired out or otherwise circulated
without the supplier's prior consent, in any form of packaging or cover
other than that in which it was produced. No part of this manual or
accompanying software may be reproduced, stored in a retrieval system on
optical or magnetic disk, tape or any other medium, or transmitted in any
form or by any means, electronic, mechanical, photocopying, recording or
otherwise for any purpose other than the purchaser's personal use.
This product is not to be used in the planning, construction, maintenance,
operation or use of any nuclear facility nor the flight, navigation or
communication of aircraft or ground support equipment. The author shall
not be liable, in whole or in part, for any claims or damages arising from
such use, including death, bancruptcy or outbreak of war.
----------------------------------------------------------------------
The IUCr Policy
for the Protection and the Promotion of the STAR File and
CIF Standards for Exchanging and Archiving Electronic Data
Overview
The Crystallographic Information File (CIF)[1] is a standard for
information interchange promulgated by the International Union of
Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the recommended
method for submitting publications to Acta Crystallographica Section C and
reports of crystal structure determinations to other sections of Acta
Crystallographica and many other journals. The syntax of a CIF is a subset
of the more general STAR File[2] format. The CIF and STAR File approaches
are used increasingly in the structural sciences for data exchange and
archiving, and are having a significant influence on these activities in
other fields.
Statement of intent
The IUCr's interest in the STAR File is as a general data interchange
standard for science, and its interest in the CIF, a conformant derivative
of the STAR File, is as a concise data exchange and archival standard for
crystallography and structural science.
Protection of the standards
To protect the STAR File and the CIF as standards for interchanging and
archiving electronic data, the IUCr, on behalf of the scientific
community,
* holds the copyrights on the standards themselves,
* owns the associated trademarks and service marks, and
* holds a patent on the STAR File.
These intellectual property rights relate solely to the interchange
formats, not to the data contained therein, nor to the software used in
the generation, access or manipulation of the data.
Promotion of the standards
The sole requirement that the IUCr, in its protective role, imposes on
software purporting to process STAR File or CIF data is that the following
conditions be met prior to sale or distribution.
* Software claiming to read files written to either the STAR File or the
CIF standard must be able to extract the pertinent data from a file
conformant to the STAR File syntax, or the CIF syntax, respectively.
* Software claiming to write files in either the STAR File, or the CIF,
standard must produce files that are conformant to the STAR File syntax,
or the CIF syntax, respectively.
* Software claiming to read definitions from a specific data dictionary
approved by the IUCr must be able to extract any pertinent definition
which is conformant to the dictionary definition language (DDL)[3]
associated with that dictionary.
The IUCr, through its Committee on CIF Standards, will assist any
developer to verify that software meets these conformance conditions.
Glossary of terms
[1] CIF:
is a data file conformant to the file syntax defined at
http://www.iucr.org/iucr-top/cif/spec/index.html
[2] STAR File:
is a data file conformant to the file syntax defined at
http://www.iucr.org/iucr-top/cif/spec/star/index.html
[3] DDL:
is a language used in a data dictionary to define data items in terms of
"attributes". Dictionaries currently approved by the IUCr, and the DDL
versions used to construct these dictionaries, are listed at
http://www.iucr.org/iucr-top/cif/spec/ddl/index.html
Last modified: 30 September 2000
IUCr Policy Copyright (C) 2000 International Union of Crystallography
----------------------------------------------------------------------
CBFlib V0.1 Notice
The following Diclaimer Notice applies to CBFlib V0.1, from which this
code is in part is derived.
* The items furnished herewith were developed under the sponsorship of
the U.S. Government. Neither the U.S., nor the U.S. D.O.E., nor the
Leland Stanford Junior University, nor their employees, makes any
warranty, express or implied, or assumes any liability or
responsibility for accuracy, completeness or usefulness of any
information, apparatus, product or process disclosed, or represents
that its use will not infringe privately-owned rights. Mention of any
product, its manufacturer, or suppliers shall not, nor is it intended
to, imply approval, disapproval, or fitness for any particular use.
The U.S. and the University at all times retain the right to use and
disseminate the furnished items for any purpose whatsoever.
Notice 91 02 01
----------------------------------------------------------------------
CIFPARSE Notice
Portions of this software are loosely based on the CIFPARSE software
package from the NDB at Rutgers university (see
http://ndbserver.rutgers.edu/NDB/mmcif/software). CIFPARSE is part of the
NDBQUERY application, a program component of the Nucleic Acid Database
Project [ H. M. Berman, W. K. Olson, D. L. Beveridge, J. K. Westbrook, A.
Gelbin, T. Demeny, S. H. Shieh, A. R. Srinivasan, and B. Schneider.
(1992). The Nucleic Acid Database: A Comprehensive Relational Database of
Three-Dimensional Structures of Nucleic Acids. Biophys J., 63, 751-759.],
whose cooperation is gratefully acknowledged, especially in the form of
design concepts created by J. Westbrook.
Please be aware of the following notice in the CIFPARSE API:
This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS
FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED.
RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE WILL NOT
INFRINGE ANY PATENT, COPYRIGHT OR OTHER PROPRIETARY RIGHT.
| OpenRasMol | Copying and Distribution | Contents | Installation Instructions |
| Changes | Things To Do | Introduction | Source Code and Binaries |
| RasMol Manual | Spanish Translation of RasMol Manual | Italian Translation of
RasMol Help File |
| Donate to Support RasMol | Release README | Register your RasMol |
----------------------------------------------------------------------
Updated 26 January 2008. yaya@bernstein-plus-sons.com
rasmol-2.7.6.0/PROJECTS 0000775 0000000 0000000 00000006666 13364034342 0014360 0 ustar 00root root 0000000 0000000 # File PROJECTS
# RasMol2, Roger Sayle
# Glaxo Research & Development
# Last Modified 28/03/95
# Any person (university or company) wishing to help with any
# of the projects described below, please e-mail the author at
# "ras32425@ggr.co.uk".
[A] Machine Independent
=======================
[A1] Input Formats
------------------
[1] BioSym's .car format (including polymer extensions).
[2] Macromodel format files.
[3] Implement STAR file parser for mmCIF,MIF and MODEL files
[3] Gaussian (z-matrix) files.
[4] DayLight Chemical System's Thor data trees (.tdt)
[5] Support for complex parsing of ASN.1 mmdb
[A2] Chemistry/Biology Support
------------------------------
[1] Priestle-style Structure Smoothing
[2] Define "cisproline" from Omega angles.
[3] Crystallographic Symmetry operators.
[4] Richardson's `typed' turn definitions (instead of DSSP)
[5] "phi" & "psi" properties of amino acid residues.
[6] "helix(3)" and "turn(2)" subtypes in expressions.
[7] "set dielectric" parameter for potential surfaces.
[8] Read default SSBOND from PDB file.
[9] Determine charges using "Marselli-Gasteiger"
[A3] Output Formats
-------------------
[1] Persistance of Vision (POV) ray tracer format
[2] Write out secondary structure to PDB files
[3] Vector PostScript output of Ribbons (MolScript)
[A5] Representations
--------------------
[1] Flat Capped Cylinder Representation
[2] Full `Connolly' Solvent Accessible Surface
[3] Solid Polygonal Solvent Surfaces [like GRASP].
[4] Priestle "Ribbons" for alpha carbon only backbones.
[5] Group (Bounding) Spheres Representation
[6] Ortep Style thermal ellipsoid Graphics.
[7] Solid `Extruded Ellipse' Representation (MIDAS & Ribbons)
[A4] Rendering
--------------
[1] Zaphod (Stereo) Mode Transformation
[2] Red-Green Stereo line drawings
[3] Improved Quality Cylinder Rendering
[4] Shadow Casting from Cylinders (IA & Quadric).
[5] Back Clipping/Slabbing Plane
[6] Shadow Casting from (Ribbon/Surface) Polygons
[A5] Misc.
----------
[1] Rewrite Manual and develop tutorial introduction.
[2] RESIZE command to set resolution even in non-iteractive mode.
[3] Increased support for MolScript & PDBregion expressions.
[4] BSD `socket'-based Inter-process Communication (OML & Flex).
[5] Optimise select expressions of the form "(atomno=%d) or (atomno=%d)"
[B] Machine & OS Dependent
==========================
[B1] UNIX & X11 Window System
-----------------------------
[1] FileOpen and FileSave Dialog Boxes
[2] X Windows Resource Database (XDefaults)
[3] Graphics Tablet and Spaceball Input
[4] X11's SGIFullScreenStereo Extension
[5] Colour 85x67 Icon for 4Dwm on SGI Machines!
[B2] MS-DOS & MS Windows 3.1
----------------------------
[1] MS Windows WINDOWS.INI File Processing
[2] DDE Transfer of Valuators
[3] Develop 32/24bit graphics version of RasWin
[B3] Apple Macintosh & PowerMac
--------------------------------
[1] Select and Copy text from the command line.
[2] Simple AppleEvents to ExecuteCommands.
[3] Advanced AppleEvents to Transfer Data.
[4] Initialisation [Preference?] File.
[B4] VAX/AXP VMS
----------------
[1] Improved filename parsing and expansion!
[2] Spawn process to uncompress files.
[B5] Other Systems
------------------
[1] Acorn Archimedes (ARM) version for UK schools.
[2] Commodore Amiga version (???).
rasmol-2.7.6.0/RASLIC 0000664 0000000 0000000 00000006036 13364034342 0014070 0 ustar 00root root 0000000 0000000
Creative endeavors depend on the lively exchange of ideas. There are laws
and customs which establish rights and responsibilities for authors and the
users of what authors create. This notice is not intended to prevent you
from using the software and documents in this package, but to ensure that
there are no misunderstandings about terms and conditions of such use.
Please read the following notice carefully. If you do not understand any
portion of this notice, please seek appropriate professional legal advice
before making use of the software and documents included in this software
package. In addition to whatever other steps you may be obliged to take to
respect the intellectual property rights of the various parties involved, if
you do make use of the software and documents in this package, please give
credit where credit is due by citing this package, its authors and the URL
or other source from which you obtained it, or equivalent primary references
in the literature with the same authors.
Some of the software and documents included within this software package are
the intellectual property of various parties, and placement in this package
does not in any way imply that any such rights have in any way been waived
or diminished.
With respect to any software or documents for which a copyright exists, ALL
RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT.
Even though the authors of the various documents and software found here
have made a good faith effort to ensure that the documents are correct and
that the software performs according to its documentation, and we would
greatly appreciate hearing of any problems you may encounter, the programs
and documents any files created by the programs are provided **AS IS**
without any warranty as to correctness, merchantability or fitness for any
particular or general use.
THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR
DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS
LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND
NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS.
Subject to your acceptance of the conditions stated above, and your respect
for the terms and conditions stated in the notices below, if you are not
going to make any modifications or create derived works, you are given
permission to freely copy and distribute this package, provided you do the
following:
* 1. Either include the complete documentation, especially the file
NOTICE, with what you distribute or provide a clear indication where
people can get a copy of the documentation; and
* 2. Give credit where credit is due citing the version and original
authors properly; and
* 3. Do not give anyone the impression that the original authors are
providing a warranty of any kind.
In addition, you may also modify this package and create derived works
provided you do the following:
* 4. Explain in your documentation how what you did differs from this
version of RasMol; and
* 5. Make your modified source code available.
rasmol-2.7.6.0/README.html 0000775 0000000 0000000 00000045527 13364034342 0015026 0 ustar 00root root 0000000 0000000
RasMol V2.7.5.2 README
RasMol 2.7.0 March 1999
RasMol 2.7.1 June 1999 RasMol 2.7.1.1 January 2001
RasMol 2.7.2 August 2000
RasMol 2.7.2.1 April 2001
RasMol 2.7.2.1.1 January 2004
RasMol 2.7.3 February 2005
RasMol 2.7.3.1 Apr 06
RasMol 2.7.4 Nov 07
RasMol 2.7.4.1 Jan 08
RasMol 2.7.4.2 Mar 08
RasMol 2.7.5 June 2009
RasMol 2.7.5.1 July 2009
RasMol 2.7.5.2 May 2011
RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
and L. Andrews (via the neartree package). Work on RasMol 2.7.5
supported in part by grant 1R15GM078077-01 from the National Institute
of General Medical Sciences (NIGMS), U.S. National Institutes of Health
and by grant ER63601-1021466-0009501 from the Office of Biological &
Environmental Research (BER), Office of Science, U. S. Department of
Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,
N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol
2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and
grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates
changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work
on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281
and EF-0312612 from the U.S. National Science Foundation and grant
DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility
of the authors and does not necessarily represent the official views of
the funding organizations.
The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
Teemu Ikonen.
and Incorporating Translations by
Author
Item
Language
Isabel Serván Martínez,
José Miguel Fernández Fernández
2.6 Manual
Spanish
José Miguel Fernández Fernández
2.7.1 Manual
Spanish
Fernando Gabriel Ranea
2.7.1 menus and messages
Spanish
Jean-Pierre Demailly
2.7.1 menus and messages
French
Giuseppe Martini, Giovanni Paolella, A. Davassi, M. Masullo, C. Liotto
2.7.1 menus and messages
2.7.1 help file
Italian
G. Pozhvanov
2.7.3 menus and messages
Russian
G. Todorov
2.7.3 menus and messages
Bulgarian
Nan Jia, G. Todorov
2.7.3 menus and messages
Chinese
Mamoru Yamanishi, Katajima Hajime
2.7.3 menus and messages
Japanese
This Release by
Herbert J. Bernstein,
Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
The original RasMol manual was created by Roger Sayle. In July 1996,
Dr. Margaret Wong of the Chemistry Department, Swinburne University
of Technology, Australia, made extensive revisions to the RasMol 2.5
manual to accurately reflect the operation of RasMol 2.6. Eric Martz
of the University of Massachusetts made further revisions. In May
1997, William McClure of Carnegie Mellon University reorganized the
HTML version of the manual into multiple sections which could be
downloaded quickly and added use of frames. Portions of the 2.7.1
version of the RasMol manual were derived with permission from
William McClure's version using Roger Sayle's rasmol.doc for
version 2.6.4 as the primary source. Changes were made in
August 2000 for RasMol version 2.7.2, January 2001 for RasMol
version 2.7.1.1 and April 2001 for RasMol version 2.7.2.1 and
February 2005 for RasMol version 2.7.3.
Documentation Last Updated 14 May 2011
Edited by Herbert J. Bernstein and Frances C. Bernstein
Translations
Thanks to the efforts of José Miguel Fernández
Fernández (Departamento
de Bioquímica y Biología Molecular. Universidad de Granada.
España (jmfernan@ugr.es)) a
translation of the
Manual for Rasmol version 2.7.1 into Spanish is now available.
La traducción española del manual de la
versión de la Dra. Wong revisada por Eric Martz fue realizada por
Isabel Serván Martínez y José Miguel Fernández
Fernández. La actual traducción del Manual de RasMol 2.7.1
ha sido realizada usando como base la anterior de RasMol 2.6 por
José Miguel Fernández Fernández.
Thanks to translations by Fernando Gabriel Ranea in late 2000
and early 2001, RasMol is now
capable of rendering most menu items and messages in Spanish.
Jean-Pierre Demailly provided French
translations of menus and messages in January 2001.
Giuseppe Martini and Giovanni Paolella
with contributions by A. Davassi, M. Masullo and C. Liotto provided Italian
translations of menus and messages in March 2001.
IMPORTANT - Copying and Distribution
This version is based directly on RasMol version 2.7.5.1,
on RasMol version 2.7.4.2,
on RasMol version 2.7.4.1,
on RasMol version 2.7.4,
on RasMol version 2.7.3.1,
on RasMol version 2.7.3, on RasMol version 2.7.2.1.1,
on RasMol version 2.7.2, on RasMol version 2.7.1, on RasMol
version 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version
2.6.4, and RasMol 2.5-ucb and 2.6-ucb.
Please read the file NOTICE for
important notices which apply to this package and for
license terms (GPL or RASLIC).
This posting is made to announce the release of RasMol version
2.7.5.2 This release is based on
RasMol 2.7.5.1.
This is a final update to the 2.7.5 series before release of the 2.7.6 release
candidates, correcting some minor bugs and speeding up surface renderings
by use of NearTree 3.1. The version of CBFlib used has also been updated.
The changes made between the 2.7.5.1 release of 23 July 2009 and the
2.7.5.2 release were:
Faster surface rendering by use of NearTree 3.1
Updates to GTK version from T. Ikonen
Use of CBFlib 0.9.2
Use of CQRlib 1.1.2
Minor bug fixes
The changes made between the 2.7.5 release candidate release of 17 July 2009
and the formal release on 23 July 2009 were:
Correction to the support for core CIF data file loads that was disabled in the
move to CBFlib in place of the internal CIF support.
Correction to the CCP4 map read logic in the case of symmetry
lines. Thanks to Marian Szebenyi for finding this bug.
Clarification to the install instructions for 64-bit unix systems.
Thanks to Marian Szebenyi and Mark Diekhans for pointing out the lack
of clarity.
The major changes from the 2.7.4.2 release to the 2.7.5 release include:
Support for SBEVSL movie commands.
Support for Lee-Richards surface approximation by contouring pseudo-Gaussian
electron densities.
Selection of atoms by proximity to map contours
Coloring of maps by the colors of neighboring atoms
Significant improvements to the GTK version by Teemu Ikonen
The 2.7.4.2 release was based on RasMol 2.7.4 and RasMol 2.7.4.1 and
RasMol 2.7.3.1,
the final reference release for the 2.7.3 series. The changes from the 2.7.3.1 release to the
2.7.4.1 release included:
Support for maps.
Message and menu translations for Russian, Bulgarian, Japanese and Chinese.
Our thanks to G. Pozhvanov, G. Todorov, Nan Jia, Mamoru Yamanishi and Katajima Hajime.
Fix torsion angle calculation as per bug report and patch by Swati Jain.
Corrections by Ladislav Michnovic to port to more platforms.
Code to read remediated PDB entries as suggested by Huanwang Yang
Updated icons.
Extended export menus.
For more detail on these and earlier changes, consult the openrasmol svn repository
on sourceforge.
For a list of open issues in this version, see
"TODO".
RasMol is a molecular graphics program intended for the visualisation
of proteins, nucleic acids and small molecules. The program is aimed at
display, teaching and generation of publication quality images. The original
program was been developed at the University of Edinburgh's
Biocomputing Research Unit and the Biomolecular Structures Group at
Glaxo Research and Development, Greenford, UK.
RasMol reads in molecular co-ordinate files in a number of formats and
interactively displays the molecule on the screen in a variety of colour
schemes and representations. Currently supported input file formats
include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl
Mol2 formats, Molecular Design Limited's (MDL) Mol file format,
Minnesota Supercomputer Center's (MSC) XMol XYZ format, CHARMm format,
MOPAC format, CIF format and mmCIF format files. If connectivity
information and/or secondary structure information is not contained in
the file this is calculated automatically. The loaded molecule may be
shown as wireframe, cylinder (drieding) stick bonds, alpha-carbon
trace, spacefilling (CPK) spheres, macromolecular ribbons (either
smooth shaded solid ribbons or parallel strands), hydrogen bonding and
dot surface. Atoms may also be labelled with arbitrary text strings.
Alternate conformers and multiple NMR models may be specially coloured
and identified in atom labels. Different parts of the molecule may be
displayed and coloured independently of the rest of the molecule or
shown in different representations simultaneously. The space filling
spheres can even be shadowed. The displayed molecule may be rotated,
translated, zoomed, z-clipped (slabbed) interactively using either the
mouse, the scroll bars, the command line or an attached dials box.
RasMol can read a prepared list of commands from a `script' file (or
via interprocess communication) to allow a given image or viewpoint to
be restored quickly. RasMol can also create a script file containing
the commands required to regenerate the current image. Finally the
rendered image may be written out in a variety of formats including
both raster and vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile
or as a MolScript input script or Kinemage.
Versions of RasMol have run on a wide range of architectures and systems
including SGI, sun4, sun3, sun386i, SGI, DEC, HP and E&S workstations, IBM
RS/6000, Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBM
PC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD),
Apple Macintosh (System 7.0 or later), PowerMac and VAX VMS (under DEC
Windows). UNIX and VMS versions require an 8bit, 24bit or 32bit X
Windows frame buffer (X11R4 or later). The X Windows version of RasMol
provides optional support for a hardware dials box and accelerated
shared memory rendering (via the XInput and MIT-SHM extensions) if
available.
Reports of builds and/or problems on various platforms appreciated.
RasMol 2.7.0 March 1999
RasMol 2.7.1 June 1999 RasMol 2.7.1.1 January 2001
RasMol 2.7.2 August 2000
RasMol 2.7.2.1 April 2001
RasMol 2.7.2.1.1 January 2004
RasMol 2.7.3 February 2005
RasMol 2.7.3.1 Apr 06
RasMol 2.7.4 Nov 07
RasMol 2.7.4.1 Jan 08
RasMol 2.7.4.2 Mar 08
RasMol 2.7.5 June 2009
RasMol 2.7.5.1 July 2009
RasMol 2.7.5.2 May 2011
RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
and L. Andrews (via the neartree package). Work on RasMol 2.7.5
supported in part by grant 1R15GM078077-01 from the National Institute
of General Medical Sciences (NIGMS), U.S. National Institutes of Health
and by grant ER63601-1021466-0009501 from the Office of Biological &
Environmental Research (BER), Office of Science, U. S. Department of
Energy. RasMol 2.7.4 incorporated changes by G. Todorov, Nan Jia,
N. Darakev, P. Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol
2.7.4 supported in part by grant 1R15GM078077-01 from the NIGMS/NIH and
grant ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates
changes by Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work
on RasMol 2.7.3 supported in part by grants DBI-0203064, DBI-0315281
and EF-0312612 from the U.S. National Science Foundation and grant
DE-FG02-03ER63601 from BER/DOE. The content is solely the responsibility
of the authors and does not necessarily represent the official views of
the funding organizations.
The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
Teemu Ikonen.
and Incorporating Translations by
Author
Item
Language
Isabel Serván Martínez,
José Miguel Fernández Fernández
2.6 Manual
Spanish
José Miguel Fernández Fernández
2.7.1 Manual
Spanish
Fernando Gabriel Ranea
2.7.1 menus and messages
Spanish
Jean-Pierre Demailly
2.7.1 menus and messages
French
Giuseppe Martini, Giovanni Paolella, A. Davassi, M. Masullo, C. Liotto
2.7.1 menus and messages
2.7.1 help file
Italian
G. Pozhvanov
2.7.3 menus and messages
Russian
G. Todorov
2.7.3 menus and messages
Bulgarian
Nan Jia, G. Todorov
2.7.3 menus and messages
Chinese
Mamoru Yamanishi, Katajima Hajime
2.7.3 menus and messages
Japanese
This Release by
Herbert J. Bernstein,
Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
The original RasMol manual was created by Roger Sayle. In July 1996,
Dr. Margaret Wong of the Chemistry Department, Swinburne University
of Technology, Australia, made extensive revisions to the RasMol 2.5
manual to accurately reflect the operation of RasMol 2.6. Eric Martz
of the University of Massachusetts made further revisions. In May
1997, William McClure of Carnegie Mellon University reorganized the
HTML version of the manual into multiple sections which could be
downloaded quickly and added use of frames. Portions of the 2.7.1
version of the RasMol manual were derived with permission from
William McClure's version using Roger Sayle's rasmol.doc for
version 2.6.4 as the primary source. Changes were made in
August 2000 for RasMol version 2.7.2, January 2001 for RasMol
version 2.7.1.1 and April 2001 for RasMol version 2.7.2.1 and
February 2005 for RasMol version 2.7.3.
Documentation Last Updated 14 May 2011
Edited by Herbert J. Bernstein and Frances C. Bernstein
Translations
Thanks to the efforts of José Miguel Fernández
Fernández (Departamento
de Bioquímica y Biología Molecular. Universidad de Granada.
España (jmfernan@ugr.es)) a
translation of the
Manual for Rasmol version 2.7.1 into Spanish is now available.
La traducción española del manual de la
versión de la Dra. Wong revisada por Eric Martz fue realizada por
Isabel Serván Martínez y José Miguel Fernández
Fernández. La actual traducción del Manual de RasMol 2.7.1
ha sido realizada usando como base la anterior de RasMol 2.6 por
José Miguel Fernández Fernández.
Thanks to translations by Fernando Gabriel Ranea in late 2000
and early 2001, RasMol is now
capable of rendering most menu items and messages in Spanish.
Jean-Pierre Demailly provided French
translations of menus and messages in January 2001.
Giuseppe Martini and Giovanni Paolella
with contributions by A. Davassi, M. Masullo and C. Liotto provided Italian
translations of menus and messages in March 2001.
IMPORTANT - Copying and Distribution
This version is based directly on RasMol version 2.7.5.1,
on RasMol version 2.7.4.2,
on RasMol version 2.7.4.1,
on RasMol version 2.7.4,
on RasMol version 2.7.3.1,
on RasMol version 2.7.3, on RasMol version 2.7.2.1.1,
on RasMol version 2.7.2, on RasMol version 2.7.1, on RasMol
version 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version
2.6.4, and RasMol 2.5-ucb and 2.6-ucb.
Please read the file NOTICE for
important notices which apply to this package and for
license terms (GPL or RASLIC).
This posting is made to announce the release of RasMol version
2.7.5.2 This release is based on
RasMol 2.7.5.1.
This is a final update to the 2.7.5 series before release of the 2.7.6 release
candidates, correcting some minor bugs and speeding up surface renderings
by use of NearTree 3.1. The version of CBFlib used has also been updated.
The changes made between the 2.7.5.1 release of 23 July 2009 and the
2.7.5.2 release were:
Faster surface rendering by use of NearTree 3.1
Updates to GTK version from T. Ikonen
Use of CBFlib 0.9.2
Use of CQRlib 1.1.2
Minor bug fixes
The changes made between the 2.7.5 release candidate release of 17 July 2009
and the formal release on 23 July 2009 were:
Correction to the support for core CIF data file loads that was disabled in the
move to CBFlib in place of the internal CIF support.
Correction to the CCP4 map read logic in the case of symmetry
lines. Thanks to Marian Szebenyi for finding this bug.
Clarification to the install instructions for 64-bit unix systems.
Thanks to Marian Szebenyi and Mark Diekhans for pointing out the lack
of clarity.
The major changes from the 2.7.4.2 release to the 2.7.5 release include:
Support for SBEVSL movie commands.
Support for Lee-Richards surface approximation by contouring pseudo-Gaussian
electron densities.
Selection of atoms by proximity to map contours
Coloring of maps by the colors of neighboring atoms
Significant improvements to the GTK version by Teemu Ikonen
The 2.7.4.2 release was based on RasMol 2.7.4 and RasMol 2.7.4.1 and
RasMol 2.7.3.1,
the final reference release for the 2.7.3 series. The changes from the 2.7.3.1 release to the
2.7.4.1 release included:
Support for maps.
Message and menu translations for Russian, Bulgarian, Japanese and Chinese.
Our thanks to G. Pozhvanov, G. Todorov, Nan Jia, Mamoru Yamanishi and Katajima Hajime.
Fix torsion angle calculation as per bug report and patch by Swati Jain.
Corrections by Ladislav Michnovic to port to more platforms.
Code to read remediated PDB entries as suggested by Huanwang Yang
Updated icons.
Extended export menus.
For more detail on these and earlier changes, consult the openrasmol svn repository
on sourceforge.
For a list of open issues in this version, see
"TODO".
RasMol is a molecular graphics program intended for the visualisation
of proteins, nucleic acids and small molecules. The program is aimed at
display, teaching and generation of publication quality images. The original
program was been developed at the University of Edinburgh's
Biocomputing Research Unit and the Biomolecular Structures Group at
Glaxo Research and Development, Greenford, UK.
RasMol reads in molecular co-ordinate files in a number of formats and
interactively displays the molecule on the screen in a variety of colour
schemes and representations. Currently supported input file formats
include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl
Mol2 formats, Molecular Design Limited's (MDL) Mol file format,
Minnesota Supercomputer Center's (MSC) XMol XYZ format, CHARMm format,
MOPAC format, CIF format and mmCIF format files. If connectivity
information and/or secondary structure information is not contained in
the file this is calculated automatically. The loaded molecule may be
shown as wireframe, cylinder (drieding) stick bonds, alpha-carbon
trace, spacefilling (CPK) spheres, macromolecular ribbons (either
smooth shaded solid ribbons or parallel strands), hydrogen bonding and
dot surface. Atoms may also be labelled with arbitrary text strings.
Alternate conformers and multiple NMR models may be specially coloured
and identified in atom labels. Different parts of the molecule may be
displayed and coloured independently of the rest of the molecule or
shown in different representations simultaneously. The space filling
spheres can even be shadowed. The displayed molecule may be rotated,
translated, zoomed, z-clipped (slabbed) interactively using either the
mouse, the scroll bars, the command line or an attached dials box.
RasMol can read a prepared list of commands from a `script' file (or
via interprocess communication) to allow a given image or viewpoint to
be restored quickly. RasMol can also create a script file containing
the commands required to regenerate the current image. Finally the
rendered image may be written out in a variety of formats including
both raster and vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile
or as a MolScript input script or Kinemage.
Versions of RasMol have run on a wide range of architectures and systems
including SGI, sun4, sun3, sun386i, SGI, DEC, HP and E&S workstations, IBM
RS/6000, Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBM
PC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD),
Apple Macintosh (System 7.0 or later), PowerMac and VAX VMS (under DEC
Windows). UNIX and VMS versions require an 8bit, 24bit or 32bit X
Windows frame buffer (X11R4 or later). The X Windows version of RasMol
provides optional support for a hardware dials box and accelerated
shared memory rendering (via the XInput and MIT-SHM extensions) if
available.
Reports of builds and/or problems on various platforms appreciated.
Updated 14 May 2011.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
rasmol-2.7.6.0/README.txt 0000664 0000000 0000000 00000044642 13364034342 0014673 0 ustar 00root root 0000000 0000000 README
RasMol 2.7.5.2
* RasMol Latest Windows * RasMol 2.7.5.2 Windows
Installer Installer
* RasMol Latest Source * RasMol 2.7.5.2 Source
Tarball RasMol Tarball
* RasMol Latest Manual * RasMol 2.7.5 Manual
* Donate to Support RasMol * Donate to Support RasMol
* Register your RasMol * Register your RasMol
Molecular Graphics Visualisation Tool
3 June 2009 (rev. 13 May 2011)
Based on RasMol 2.6 by Roger Sayle
Biomolecular Structures Group, Glaxo Wellcome Research & Development, Stevenage,
Hertfordshire, UK
Version 2.6, August 1995, Version 2.6.4, December 1998
Copyright (c) Roger Sayle 1992-1999
and Based on Mods by
+------------------------------------------------------------------------------+
| Author | Version, Date | Copyright |
|-------------------+----------------------+-----------------------------------|
| Arne Mueller | RasMol 2.6x1 May | (c) Arne Mueller 1998 |
| | 1998 | |
|-------------------+----------------------+-----------------------------------|
| Gary Grossman and | RasMol 2.5-ucb | (c) UC Regents/ModularCHEM |
| Marco Molinaro | November 1995 | Consortium 1995, 1996 |
| | RasMol 2.6-ucb | |
| | November 1996 | |
|-------------------+----------------------+-----------------------------------|
| Philippe Valadon | RasTop 1.3 August | (c) Philippe Valadon 2000 |
| | 2000 | |
|-------------------+----------------------+-----------------------------------|
| Herbert J. | RasMol 2.7.0 March | (c) Herbert J. Bernstein |
| Bernstein | 1999 | 1998-2009 |
| | RasMol 2.7.1 June | |
| | 1999 | |
| | RasMol 2.7.1.1 | |
| | January 2001 | |
| | RasMol 2.7.2 August | |
| | 2000 | |
| | RasMol 2.7.2.1 April | |
| | 2001 | |
| | RasMol 2.7.2.1.1 | |
| | January 2004 | |
| | RasMol 2.7.3 | |
| | February 2005 | |
| | RasMol 2.7.3.1 Apr | |
| | 06 | |
| | RasMol 2.7.4 Nov 07 | |
| | RasMol 2.7.4.1 Jan | |
| | 08 | |
| | RasMol 2.7.4.2 Mar | |
| | 08 | |
| | RasMol 2.7.5 June | |
| | 2009 | |
| | RasMol 2.7.5.1 July | |
| | 2009 | |
| | RasMol 2.7.5.2 May | |
| | 2011 | |
+------------------------------------------------------------------------------+
RasMol 2.7.5 incorporates changes by T. Ikonen, G. McQuillan, N. Darakev
and L. Andrews (via the neartree package). Work on RasMol 2.7.5 supported
in part by grant 1R15GM078077-01 from the National Institute of General
Medical Sciences (NIGMS), U.S. National Institutes of Health and by grant
ER63601-1021466-0009501 from the Office of Biological & Environmental
Research (BER), Office of Science, U. S. Department of Energy. RasMol
2.7.4 incorporated changes by G. Todorov, Nan Jia, N. Darakev, P.
Kamburov, G. McQuillan, and J. Jemilawon. Work on RasMol 2.7.4 supported
in part by grant 1R15GM078077-01 from the NIGMS/NIH and grant
ER63601-1021466-0009501 from BER/DOE. RasMol 2.7.3 incorporates changes by
Clarice Chigbo, Ricky Chachra, and Mamoru Yamanishi. Work on RasMol 2.7.3
supported in part by grants DBI-0203064, DBI-0315281 and EF-0312612 from
the U.S. National Science Foundation and grant DE-FG02-03ER63601 from
BER/DOE. The content is solely the responsibility of the authors and does
not necessarily represent the official views of the funding organizations.
The code for use of RasMol under GTK in RasMol 2.7.4.2 was written by
Teemu Ikonen.
and Incorporating Translations by
+-----------------------------------------------------------------------------+
| Author | Item | Language |
|--------------------------------------+--------------------------+-----------|
| Isabel Servan Martinez, | 2.6 Manual | Spanish |
| Jose Miguel Fernandez Fernandez | | |
|--------------------------------------+--------------------------+-----------|
| Jose Miguel Fernandez Fernandez | 2.7.1 Manual | Spanish |
|--------------------------------------+--------------------------+-----------|
| Fernando Gabriel Ranea | 2.7.1 menus and messages | Spanish |
|--------------------------------------+--------------------------+-----------|
| Jean-Pierre Demailly | 2.7.1 menus and messages | French |
|--------------------------------------+--------------------------+-----------|
| Giuseppe Martini, Giovanni Paolella, | 2.7.1 menus and messages | Italian |
| A. Davassi, M. Masullo, C. Liotto | 2.7.1 help file | |
|--------------------------------------+--------------------------+-----------|
| G. Pozhvanov | 2.7.3 menus and messages | Russian |
|--------------------------------------+--------------------------+-----------|
| G. Todorov | 2.7.3 menus and messages | Bulgarian |
|--------------------------------------+--------------------------+-----------|
| Nan Jia, G. Todorov | 2.7.3 menus and messages | Chinese |
|--------------------------------------+--------------------------+-----------|
| Mamoru Yamanishi, Katajima Hajime | 2.7.3 menus and messages | Japanese |
+-----------------------------------------------------------------------------+
This Release by
Herbert J. Bernstein, Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
yaya@bernstein-plus-sons.com
Copyright (c) Herbert J. Bernstein 1998-2009
The original RasMol manual was created by Roger Sayle. In July 1996, Dr.
Margaret Wong of the Chemistry Department, Swinburne University of
Technology, Australia, made extensive revisions to the RasMol 2.5 manual
to accurately reflect the operation of RasMol 2.6. Eric Martz of the
University of Massachusetts made further revisions. In May 1997, William
McClure of Carnegie Mellon University reorganized the HTML version of the
manual into multiple sections which could be downloaded quickly and added
use of frames. Portions of the 2.7.1 version of the RasMol manual were
derived with permission from William McClure's version using Roger Sayle's
rasmol.doc for version 2.6.4 as the primary source. Changes were made in
August 2000 for RasMol version 2.7.2, January 2001 for RasMol version
2.7.1.1 and April 2001 for RasMol version 2.7.2.1 and February 2005 for
RasMol version 2.7.3.
Documentation Last Updated 14 May 2011
Edited by Herbert J. Bernstein and Frances C. Bernstein
Translations
Thanks to the efforts of Jose Miguel Fernandez Fernandez (Departamento de
Bioquimica y Biologia Molecular. Universidad de Granada. Espana
(jmfernan@ugr.es)) a translation of the Manual for Rasmol version 2.7.1
into Spanish is now available. La traduccion espanola del manual de la
version de la Dra. Wong revisada por Eric Martz fue realizada por Isabel
Servan Martinez y Jose Miguel Fernandez Fernandez. La actual traduccion
del Manual de RasMol 2.7.1 ha sido realizada usando como base la anterior
de RasMol 2.6 por Jose Miguel Fernandez Fernandez.
Thanks to translations by Fernando Gabriel Ranea
in late 2000 and early 2001, RasMol is now capable of rendering most menu
items and messages in Spanish. Jean-Pierre Demailly
provided French translations of
menus and messages in January 2001. Giuseppe Martini
and Giovanni Paolella
with contributions by A. Davassi, M. Masullo and C. Liotto provided
Italian translations of menus and messages in March 2001.
----------------------------------------------------------------------
IMPORTANT - Copying and Distribution
This version is based directly on RasMol version 2.7.5.1, on RasMol
version 2.7.4.2, on RasMol version 2.7.4.1, on RasMol version 2.7.4, on
RasMol version 2.7.3.1, on RasMol version 2.7.3, on RasMol version
2.7.2.1.1, on RasMol version 2.7.2, on RasMol version 2.7.1, on RasMol
version 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version 2.6.4, and
RasMol 2.5-ucb and 2.6-ucb.
Please read the file NOTICE for important notices which apply to this
package and for license terms (GPL or RASLIC).
----------------------------------------------------------------------
Contents
* IMPORTANT - Copying and Distribution
* Installation Instructions
* Changes
* Things To Do
* Introduction
* Source Code and Binaries
* Directories
* ChangeLog -- Full ChangeLog directory
* src -- source code
* mac -- Macintosh build directory
* mswin -- Windows build directory
* doc -- documentation
* data -- sample data files
----------------------------------------------------------------------
Introduction
This posting is made to announce the release of RasMol version 2.7.5.2
This release is based on RasMol 2.7.5.1.
This is a final update to the 2.7.5 series before release of the 2.7.6
release candidates, correcting some minor bugs and speeding up surface
renderings by use of NearTree 3.1. The version of CBFlib used has also
been updated. The changes made between the 2.7.5.1 release of 23 July 2009
and the 2.7.5.2 release were:
* Faster surface rendering by use of NearTree 3.1
* Updates to GTK version from T. Ikonen
* Use of CBFlib 0.9.2
* Use of CQRlib 1.1.2
* Minor bug fixes
The changes made between the 2.7.5 release candidate release of 17 July
2009 and the formal release on 23 July 2009 were:
* Correction to the support for core CIF data file loads that was
disabled in the move to CBFlib in place of the internal CIF support.
* Correction to the CCP4 map read logic in the case of symmetry lines.
Thanks to Marian Szebenyi for finding this bug.
* Clarification to the install instructions for 64-bit unix systems.
Thanks to Marian Szebenyi and Mark Diekhans for pointing out the lack
of clarity.
The major changes from the 2.7.4.2 release to the 2.7.5 release include:
* Support for SBEVSL movie commands.
* Support for Lee-Richards surface approximation by contouring
pseudo-Gaussian electron densities.
* Selection of atoms by proximity to map contours
* Coloring of maps by the colors of neighboring atoms
* Significant improvements to the GTK version by Teemu Ikonen
The 2.7.4.2 release was based on RasMol 2.7.4 and RasMol 2.7.4.1 and
RasMol 2.7.3.1, the final reference release for the 2.7.3 series. The
changes from the 2.7.3.1 release to the 2.7.4.1 release included:
* Support for maps.
* Message and menu translations for Russian, Bulgarian, Japanese and
Chinese. Our thanks to G. Pozhvanov, G. Todorov, Nan Jia, Mamoru
Yamanishi and Katajima Hajime.
* Fix torsion angle calculation as per bug report and patch by Swati
Jain.
* Corrections by Ladislav Michnovic to port to more platforms.
* Code to read remediated PDB entries as suggested by Huanwang Yang
* Updated icons.
* Extended export menus.
For more detail on these and earlier changes, consult the openrasmol svn
repository on sourceforge.
This version is available for MS Windows and various unix-systems. As
binaries become available, they will be released on
http://blondie.dowling.edu/projects/rasmol and
http:/www.sourceforge.net/projects/openrasmol.
For installation instructions see "INSTALL".
For a list of open issues in this version, see "TODO".
RasMol is a molecular graphics program intended for the visualisation of
proteins, nucleic acids and small molecules. The program is aimed at
display, teaching and generation of publication quality images. The
original program was been developed at the University of Edinburgh's
Biocomputing Research Unit and the Biomolecular Structures Group at Glaxo
Research and Development, Greenford, UK.
RasMol reads in molecular co-ordinate files in a number of formats and
interactively displays the molecule on the screen in a variety of colour
schemes and representations. Currently supported input file formats
include Brookhaven Protein Databank (PDB), Tripos' Alchemy and Sybyl Mol2
formats, Molecular Design Limited's (MDL) Mol file format, Minnesota
Supercomputer Center's (MSC) XMol XYZ format, CHARMm format, MOPAC format,
CIF format and mmCIF format files. If connectivity information and/or
secondary structure information is not contained in the file this is
calculated automatically. The loaded molecule may be shown as wireframe,
cylinder (drieding) stick bonds, alpha-carbon trace, spacefilling (CPK)
spheres, macromolecular ribbons (either smooth shaded solid ribbons or
parallel strands), hydrogen bonding and dot surface. Atoms may also be
labelled with arbitrary text strings. Alternate conformers and multiple
NMR models may be specially coloured and identified in atom labels.
Different parts of the molecule may be displayed and coloured
independently of the rest of the molecule or shown in different
representations simultaneously. The space filling spheres can even be
shadowed. The displayed molecule may be rotated, translated, zoomed,
z-clipped (slabbed) interactively using either the mouse, the scroll bars,
the command line or an attached dials box. RasMol can read a prepared list
of commands from a `script' file (or via interprocess communication) to
allow a given image or viewpoint to be restored quickly. RasMol can also
create a script file containing the commands required to regenerate the
current image. Finally the rendered image may be written out in a variety
of formats including both raster and vector PostScript, GIF, PPM, BMP,
PICT, Sun rasterfile or as a MolScript input script or Kinemage.
Versions of RasMol have run on a wide range of architectures and systems
including SGI, sun4, sun3, sun386i, SGI, DEC, HP and E&S workstations, IBM
RS/6000, Cray, Sequent, DEC Alpha (OSF/1, OpenVMS and Windows NT), IBM PC
(under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD), Apple
Macintosh (System 7.0 or later), PowerMac and VAX VMS (under DEC Windows).
UNIX and VMS versions require an 8bit, 24bit or 32bit X Windows frame
buffer (X11R4 or later). The X Windows version of RasMol provides optional
support for a hardware dials box and accelerated shared memory rendering
(via the XInput and MIT-SHM extensions) if available.
Reports of builds and/or problems on various platforms appreciated.
----------------------------------------------------------------------
Source Code and Binaries
The complete source code and user documentation of RasMol 2.7.5.2 may be
obtained http://www.sourceforge.net/projects/rasmol. and by anonymous FTP
at:
ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.5.2.tar.gz
or on the web at:
http://www.bernstein-plus-sons.com/software/RasMol_2.7.5.2.tar.gz
http://www.sourceforge.net/projects/rasmol.
Any comments, suggestions or questions about this modified version of
RasMol should be directed to rasmol@bernstein-plus-sons.com.
| OpenRasMol | Copying and Distribution | Contents | Installation Instructions |
| Changes | Things To Do | Introduction | Source Code and Binaries |
| RasMol Manual | Spanish Translation of RasMol Manual | Italian Translation of
RasMol 2.7.1 Help File |
| Donate to Support RasMol | Release README | Register your RasMol |
----------------------------------------------------------------------
Updated 14 May 2011.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com
rasmol-2.7.6.0/TODO.html 0000775 0000000 0000000 00000026561 13364034342 0014633 0 ustar 00root root 0000000 0000000
RasMol V2.7.4 TODO
RasMol 2.7.0 March 1999
RasMol 2.7.1 June 1999 RasMol 2.7.1.1 January 2001
RasMol 2.7.2 August 2000 RasMol 2.7.2.1 April 2001
RasMol 2.7.2 August 2000 RasMol 2.7.2.1 April 2001
RasMol 2.7.2.1.1 January 2004
RasMol 2.7.3 February 2005
RasMol 2.7.3.1 Apr 06
RasMol 2.7.4 Nov 07
RasMol 2.7.4.1 Jan 08
RasMol 2.7.4.2 Mar 08
RasMol 2.7.3 incorporates changes by Clarice Chigbo, Ricky Chachra,
and Mamoru Yamanishi. Work on RasMol 2.7.3 supported in part by
grants DBI-0203064, DBI-0315281 and EF-0312612 from the U.S. National
Science Foundation and grant DE-FG02-03ER63601 from the U.S. Department
of Energy. RasMol 2.7.4 incorporates changes by G. Todorov, Nan Jia,
N. Darakev, P. Kamburov, G. McQuillan, J. Jemilawon. Work on RasMol
2.7.4 supported in part by grant 1R15GM078077-01 from the National
Institute of General Medical Sciences (NIGMS). The content is solely
the responsibility of the authors and does not necessarily represent
the official views of the funding organizations.
and Incorporating Translations by
Author
Item
Language
Isabel Serván Martínez,
José Miguel Fernández Fernández
2.6 Manual
Spanish
José Miguel Fernández Fernández
2.7.1 Manual
Spanish
Fernando Gabriel Ranea
2.7.1 menus and messages
Spanish
Jean-Pierre Demailly
2.7.1 menus and messages
French
Giuseppe Martini, Giovanni Paolella, A. Davassi, M. Masullo, C. Liotto
2.7.1 menus and messages
2.7.1 help file
Italian
G. Pozhvanov
2.7.3 menus and messages
Russian
G. Todorov
2.7.3 menus and messages
Bulgarian
Nan Jia, G. Todorov
2.7.3 menus and messages
Chinese
Mamoru Yamanishi, Katajima Hajime
2.7.3 menus and messages
Japanese
This Release by
Herbert J. Bernstein,
Bernstein + Sons, 5 Brewster Lane, Bellport, NY, USA
The original RasMol manual was created by Roger Sayle. In July 1996,
Dr. Margaret Wong of the Chemistry Department, Swinburne University
of Technology, Australia, made extensive revisions to the RasMol 2.5
manual to accurately reflect the operation of RasMol 2.6. Eric Martz
of the University of Massachusetts made further revisions. In May
1997, William McClure of Carnegie Mellon University reorganized the
HTML version of the manual into multiple sections which could be
downloaded quickly and added use of frames. Portions of the 2.7.1
version of the RasMol manual were derived with permission from
William McClure's version using Roger Sayle's rasmol.doc for
version 2.6.4 as the primary source. Changes were made in
August 2000 for RasMol version 2.7.2, January 2001 for RasMol
version 2.7.1.1 and April 2001 for RasMol version 2.7.2.1 and
February 2005 for RasMol version 2.7.3.
Documentation Last Updated 12 November 2007
Edited by Herbert J. Bernstein and Frances C. Bernstein
Translations
Thanks to the efforts of José Miguel Fernández
Fernández (Departamento
de Bioquímica y Biología Molecular. Universidad de Granada.
España (jmfernan@ugr.es)) a
translation of the
Manual for Rasmol version 2.7.1 into Spanish is now available.
La traducción española del manual de la
versión de la Dra. Wong revisada por Eric Martz fue realizada por
Isabel Serván Martínez y José Miguel Fernández
Fernández. La actual traducción del Manual de RasMol 2.7.1
ha sido realizada usando como base la anterior de RasMol 2.6 por
José Miguel Fernández Fernández.
Thanks to translations by Fernando Gabriel Ranea in late 2000
and early 2001, RasMol is now
capable of rendering most menu items and messages in Spanish.
Jean-Pierre Demailly provided French
translations of menus and messages in January 2001.
Giuseppe Martini and Giovanni Paolella
with contributions by A. Davassi, M. Masullo and C. Liotto provided Italian
translations of menus and messages in March 2001.
THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS
***** USE WITH CAUTION ******
IMPORTANT - Copying and Distribution
This version is based in directly on RasMol version 2.7.2.1.1,
on RasMol version 2.7.2, on RasMol version 2.7.1, on RasMol
version 2.6_CIF.2, on RasMol version 2.6x1, on RasMol version
2.6.4, and RasMol 2.5-ucb and 2.6-ucb.
Please read the file NOTICE for
important notices which apply to this package and for
license terms (GPL or RASLIC).
Combining RasMol Variants
The first steps in combining RasMol variants have been performed.
Much of the work of upgrading the documentation has been done. It
remains to make the changes to prepdoc to generate the RasFrames
version.
Several source mod packages are being reviewed for inclusion.
Features
from other variants of RasMol will be considered for inclusion in RasMol
2.7.n if the features are particularly popular and if available resources
(or helpful colleagues) make inclusion of those features feasible. When we
are done, probably in the early fall, the resulting best version should be
a reasonably stable and reliable single version combining most of the
features of the major current variants of RasMol.
Some other important things still to be done
Add code to read mmCIF templates
Add code for VRML ribbons
Add code for CBFlib map write/read
Add P. Zhivkov's blurring to simulate surfaces.
Add OpenGL management of images.
Make native Mac OS X version.
Add smooth double buffering to switch molecules for movies.
Fix problems with very large zoom scale.
Add GUI toolbar interface.
Resolve color management issues (including auto-sensing bit depth).
Fix printing under windows.
Allow for longer names.
CIF and mmCIF write logic.
The read logic for large NMR structures on a Mac needs to be made to work.
The field widths for alternate conformer ID's and chains need to be
extended to allow for the more flexible naming in mmCIF.
Resolve problem with interaction of stereo and shadows.
Allow writing of GIFs from high colour-resolution mode.
Improve memory management on Macs to allow larger structures.