                                   README
                               RasMol 2.7.2.1

                    Molecular Graphics Visualisation Tool
                                14 April 2001

                     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
 Author             Version, Date             Copyright
 Arne Mueller       RasMol 2.6x1   May 98     (C) Arne Mueller 1998
 Gary Grossman and  RasMol 2.5-ucb Nov 95     (C) UC Regents/ModularCHEM
 Marco Molinaro     RasMol 2.6-ucb Nov 96         Consortium 1995, 1996

 Philippe Valadon   RasTop 1.3     Aug 00     (C) Philippe Valadon 2000

 Herbert J.         RasMol 2.7.0   Mar 99     (C) Herbert J. Bernstein 1998-2001
 Bernstein          RasMol 2.7.1   Jun 99
                    RasMol 2.7.1.1 Jan 01
                    RasMol 2.7.2   Aug 00
                    RasMol 2.7.2.1 Apr 01

                     and Incorporating Translations by
   Author                               Item                      Language
   Isabel Servn Martnez,
   Jos Miguel Fernndez Fernndez      2.6   Manual              Spanish
   Jos Miguel Fernndez Fernndez      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
   A. Davassi, M. Masullo, C. Liotto    2.7.1 help file           Italian

                              This Release by
   Herbert J. Bernstein, Bernstein + Sons, P.O. Box 177, Bellport, NY, USA
                        yaya@bernstein-plus-sons.com
                 Copyright(C) Herbert J. Bernstein 1998-2001

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.

                   Documentation Last Updated 21 April 2001
          Edited by Herbert J. Bernstein and Frances C. Bernstein

                                Translations

Thanks to the efforts of Jos Miguel Fernndez Fernndez (Departamento de
Bioqumica y Biologa Molecular. Universidad de Granada. Espaa
(jmfernan@ugr.es)) a translation of the Manual for Rasmol version 2.7.1 into
Spanish is now available. La traduccin espaola del manual de la versin de
la Dra. Wong revisada por Eric Martz fue realizada por Isabel Servn
Martnez y Jos Miguel Fernndez Fernndez. La actual traduccin del Manual
de RasMol 2.7.1 ha sido realizada usando como base la anterior de RasMol 2.6
por  Jos Miguel Fernndez Fernndez.

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 ******

This is a preliminary release of a version from the RasMol 2.7 series
incorporating the "UCB" mods and other major changes. It is being released
at this stage to solicit comments and suggestions, and is not intended for
production use at this time.
  ------------------------------------------------------------------------

                    IMPORTANT - Copying and Distribution

This version is based directly on RasMol version 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. 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.
  ------------------------------------------------------------------------

                                  Contents

   * IMPORTANT - Copying and Distribution
   * Installation Instructions
   * Changes
   * Things To Do
   * Introduction
   * Source Code and Binaries
   * Directories
        o ChangeLog -- Full ChangeLog directory
        o src -- source code
             + mac -- Macintosh build directory
             + mswin -- Windows build directory
        o doc -- documentation
        o data -- sample data files

  ------------------------------------------------------------------------

                                Introduction

Note: Post release patches to command.c have been 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.

This posting is to announce the release of RasMol version 2.7.2.1, which
makes the following changes to RasMol 2.7.2, incorporating changes from
RasMol 2.7.1.1 and some changes from RasTop 1.3:

   * 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.

The release of RasMol version 2.7.1.1 made the following changes to RasMol
2.7.1:

   * 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.

This was an interim release to facillitate testing of the new multilingual
capabilities. Our thanks to Fernando Gabriel Ranea for doing the hard work
of creating an initial Spanish translation of RasMol 2.7.1. We have created
this new version to allow on-the-fly switching among langauges. Use the
command "Spanish" to request Spanish messages and menus, and "English" to
return to the original English format. Corrections and translations for
additional languages greatly appreciated.

The release of RasMol version 2.7.2, made the following changes to RasMol
2.7.1:

   * 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.

This release does not include the toolbar from the UCB mods. In order to
resolve some cross-platform issues we have started incorporation of the UCB
code for multiple molecules and bond rotation by adding to the command
interface and to the menus. We expect to be able to add a toolbar in a
future release.

This release is not fully debugged and has some serious problems. This
release is intended for testing and experimentation and not for production
use. Comments and suggestions would be appreciated. We are aware fo the
following deficiencies:

   * RasMol may have difficulty in allocating colors for molecules after the
     first. The fix for this interacts with some other pending changes, and
     should be ready for the next release.
   * As has been true for all recent versions, the stereo mode defaults to
     cross-eyed, which is inconvenient for many users. The next release will
     allow cross-eyed and wall-eyed stereo to be selected from the menus.
   * Printing under windows is not working for many modern systems. We hope
     to have a fix for the next release.
   * The fixes for several of the bugs reported against RasMol 2.7.1 have
     not been incorporated into RasMol 2.7.2 yet. Our apologies. If you
     previously reported a bug in RasMol 2.7.1 which still exists in 2.7.2,
     you may resubmit your report, but there is no need to do so.

The release of RasMol version 2.7.1 made the following changes to RasMol
2.7.0:

   * 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.

RasMol version 2.7.0.1 was a technically minor, but operationally critical
upgrade to version 2.7.0, correcting a serious error in the selection logic
introduced in the process of merging versions to create version 2.7.0.

RasMol version 2.7.0 combined Roger Sayle's version 2.6.4 with Herbert
Bernstein's CIF modified version 2.6_CIF(Rev 2) and with Arne Mueller's
version 2.6x1. This combined version allows selection by alternate
conformers as well as by models, production of Ramachandran printer plots
(as in F. Bernstein's fisipl), and access to A. Mueller's POVray output as
POVray3 in addition to the existing POVray version 2 output. (POVray3 should
not be used in the PC or Mac version, yet).

RasMol version 2.6x1 was an upgrade to RasMol by Arne Mueller to add code to
allow listing of information about the chains, groups or atoms in a
selection, listing of phi-psi, allow selection by cis angle cutoff, and to
provide a POV-Ray version 3 output.

RasMol version 2.6.4 was a major code cleanup and reorganization by Roger
Sayle, dropping obsolete non-ANSI C options and providing speed improvments.

RasMol version 2.6_CIF(Rev 2) added pre-compiled binaries for OpenVMS 7.1
(DEC Alpha) and OpenVMS 6.2 (DEC VAX) and replaced the binary for 68K Apple
MacIntoshes in RasMol version 2.6_CIF(Rev 1).

Rasmol version 2.6_CIF(Rev 1) was a minor update to RasMol version 2.6_CIF,
which added support for alternate conformer coloring of small molecule CIFs,
using _atom_site_disorder_group, recognizes requests for bonds which have
neither atom names nor atom numbers, ensures zapping of existing bonds when
connect command is used.

RasMol version 2.6_CIF added several new features to RasMol:

   * Support for reading IUCr CIF and mmCIF format;
   * Coloring for alternate conformers and multiple NMR models;
   * Display of all NMR models in a data set.

This version is available for the Apple Macintosh and PowerMac in addition
to UNIX, VMS and Microsoft Windows versions. However, because of limitations
in the memory management under MacOS, very large multiple NMR model datasets
are not supported on the Mac or PowerMac at this time.

For a complete list of changes from RasMol 2.6 refer to the distribution's
"ChangeLog".

For installation instructions see "INSTALL".

For a list of open issues in this version, see "TODO". Roger Sayle's prior
list of pending projects is in "PROJECTS".

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 program
has 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.

RasMol will 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.

As of this writing (5 April 2001), this version has been built for Mandrake
7.2 Linux, SGI, Mac, and IBM PC under Windows 95/98. Reports of builds
and/or problems on other platforms appreciated.

  ------------------------------------------------------------------------

                          Source Code and Binaries

The complete source code and user documentation of RasMol 2.7.2.1 may be
obtained by anonymous FTP at:

ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.2.1.tar.gz

or on the web at:

http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1.tar.gz

The source code and documentation are stored in several files appropriate
for the receiving operating system. Please read the "README" file in the
distribution directory. See the table below for appropriate binaries. Mac
and Windows binaries are no longer included on the tar. Unix and VMS users
should retrieve the same file for source code and documentation, and one or
more of the following pre-compiled binaries: WARNING: ALL binaries are
gzipped!!!

 System     Binary                                          Help Files
 Linux (Mandrake 7.2, i386):
            RasMol.LINUX/Mandrake_7.2/i386/rasmol_8BIT.gz   rasmol.hlp.gz
            RasMol.LINUX/Mandrake_7.2/i386/rasmol_16BIT.gz  rasmol.hlp.gz
            RasMol.LINUX/Mandrake_7.2/i386/rasmol_32BIT.gz  rasmol.hlp.gz

 Mac:       RasMac_FAT_8BIT.bin.gz                          rasmol.hlp.gz
            RasMac_PPC_8BIT.bin.gz
            RasMac_68K_8BIT.bin.gz
            RasMac_FAT_32BIT.bin.gz
            RasMac_PPC_32BIT.bin.gz
            RasMac_68K_32BIT.bin.gz


 Windows:   RasWin.exe.gz                                   rasmol.hlp.gz,
                                                            raswin.hlp.gz

For those who have difficulty downloading "gzipped" files, uncompressed
files are available:
 System         Binary                                       Help Files
 Linux (Mandrake 7.2, i386):
                RasMol.LINUX/Mandrake_7.2/i386/rasmol_8BIT   rasmol.hlp
                RasMol.LINUX/Mandrake_7.2/i386/rasmol_16BIT  rasmol.hlp
                RasMol.LINUX/Mandrake_7.2/i386/rasmol_32BIT  rasmol.hlp

 Mac:           RasMac_FAT_8BIT.bin                          rasmol.hlp
                RasMac_PPC_8BIT.bin
                RasMac_68K_8BIT.bin
                RasMac_FAT_32BIT.bin
                RasMac_PPC_32BIT.bin
                RasMac_68K_32BIT.bin


 Windows:       RasWin.exe                                   rasmol.hlp,
                                                             raswin.hlp

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.

Please remember to use "binary" mode when transferring these files between
systems. Check that the file size is the same before and after transfer.

Any comments, suggestions or questions about this modified version of RasMol
should be directed to rasmol@bernstein-plus-sons.com.

  ------------------------------------------------------------------------
Updated 10 July 2001.
Herbert J. Bernstein
Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
yaya@bernstein-plus-sons.com
+1-631-286-1339
