                                     README
                                RasMol 2.7.2.1.1

                      Molecular Graphics Visualisation Tool
                                 26 January 2004

                       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
   Marco Molinaro          RasMol 2.5-ucb November 1995
                           RasMol 2.6-ucb November 1996 
                             (C) UC Regents/ModularCHEM
                             Consortium 1995, 1996
   Philippe Valadon        RasTop 1.3 August 2000
                             (C)  Philippe Valadon 2000
   Herbert J. Bernstein    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
                             (C) Herbert J. Bernstein 1998-2004

                        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,
   A. Davassi, M. Masullo, C. Liotto 2.7.1 menus and messages
   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.
     ______________________________________________________________________

                               Production Release

   RasMol 2.7.2.1.1 is the production release of version 2.7.2 of the RasMol
   2.7 series. Aside from code cleanups to avoid compiler warning messages,
   and one bug fix (to allow reading of the RCSB PDB mmCIF extensions data
   sets), this release is the same as the April 2001 2.7.1.1 release. 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. People who
   downloaded raswin.exe prior to 7 May 2004 should redo the download.
     ______________________________________________________________________

                      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
          + ChangeLog -- Full ChangeLog directory
          + src -- source code
               o mac -- Macintosh build directory
               o mswin -- Windows build directory
          + doc -- documentation
          + data -- sample data files
     ______________________________________________________________________

                                  Introduction

   Note: The 2.7.2.1.1 is the final reference release for the 2.7.2 series
   prior to the creation of version 2.7.3. For most users there should be no
   operational changes from version 2.7.2.1, except for the correction to the
   loading of PDB exchange dictionary CIFS.

   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.

   The April 2001 posting was made to announce the release of RasMol version
   2.7.2.1, which made 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.

   That 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 (16 February 2004), this version has been built for
   RedHat 7 Linux, SGI, AIX, 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 2.7.2.1.1 may be
   obtained by anonymous FTP at:

   ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.2.1.1.tar.gz

   or on the web at:

   http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1.1.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!!!. Uncompressed binaries are also available in the second section
   of each page.

                      DEC/Compaq/HP:          RasMol.DEC
                      HP:                     RasMol.HP
                      Linux (RedHat 7, i386): RasMol.LINUX
                      Mac:                    RasMol.MAC
                      MS Windows:             RasMol.MSWIN
                      RS/6000:                RasMol.RS6K
                      SGI:                    RasMol.SGI

   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.

        | 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 |
                               | Release README |
     ______________________________________________________________________

   Updated 7 May 2004.
   Herbert J. Bernstein
   Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
   yaya@bernstein-plus-sons.com
