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Source Code and Binaries |
| RasMol Manual |
Release README |
ChangeLog
RasMol 2.7.1
Molecular Graphics Visualisation Tool
22 June 1999
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 © Roger Sayle 1992-1999
and Based on Mods by Arne Mueller
Version 2.6x1, May 1998
Copyright © Arne Mueller 1998
Version 2.7.0, 2.7.1 Mods
by
Herbert J. Bernstein
Bernstein + Sons,
P.O. Box 177, Bellport, NY, USA,
yaya@bernstein-plus-sons.com
2.7.0 March 1999, 2.7.1 June 1999
Copyright © Herbert J. Bernstein 1998-1999
THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS
***** USE WITH CAUTION ******
IMPORTANT
This version is based on RasMol version 2.6_CIF.2, on RasMol version
2.6x1 and on RasMol version 2.6.4. Please read the file NOTICE for
important notices which apply to this package. If you are not going to
make changes to RasMol, you are not only permitted to freely make copies
and distribute them, you are encouraged to do so, 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. Please give credit where credit is due citing the version and
original authors properly; and
- 3. Please do not give anyone the impression that the original authors
are providing a warranty of any kind.
If you would like to use major pieces of RasMol in some other program, make
modifications to RasMol, or in some other way make what a lawyer would call
a "derived work", you are not only permitted to do so, you are encouraged
to do so. In addition to the things we discussed above, please do the
following:
- 4. Please explain in your documentation how what you did differs from
this version of RasMol; and
- 5. Please make your modified source code available.
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 2.7.0.1 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
| Copying and Distribution |
Contents |
Installation Instructions |
| Changes |
Things To Do |
Introduction |
Source Code and Binaries |
| RasMol Manual |
Release README |
Updated 15 July 1999.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com
+1-516-286-1339
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