                                          README
                                       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 1998      | (c) Arne Mueller 1998              |
|----------------------+----------------------------+------------------------------------|
| Gary Grossman and    | RasMol 2.5-ucb November    | (c) UC Regents/ModularCHEM         |
| Marco Molinaro       | 1995                       | Consortium 1995, 1996              |
|                      | RasMol 2.6-ucb November    |                                    |
|                      | 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 1998-2009 |
|                      | 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 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 <davinci@dinamica.com.ar> in late
   2000 and early 2001, RasMol is now capable of rendering most menu items and messages
   in Spanish. Jean-Pierre Demailly <Jean-Pierre.Demailly@ujf-grenoble.fr> provided
   French translations of menus and messages in January 2001. Giuseppe Martini
   <martini@iigb.na.cnr.it> and Giovanni Paolella <paolella@dbbm.unina.it> 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 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).

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

  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. This release
   is based on RasMol 2.7.4.2, the final reference release for the 2.7.4 series. 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 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.tar.gz

   or on the web at:

   http://www.bernstein-plus-sons.com/software/RasMol_2.7.5.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 19 July 2009.
                                   Herbert J. Bernstein
             Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
                               yaya@bernstein-plus-sons.com

References

   Visible links
   . http://www.iucr.org/iucr-top/welcome.html
   . http://www.iucr.org/iucr-top/cif/home.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/doc/rasmol.html
   . http://www.openrasmol.org/
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#Copying
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#Contents
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/INSTALL.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/ChangeLog.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/TODO.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#Introduction
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#CodeAndBinaries
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/doc/rasmol.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/doc/esrasmol27.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/doc/itrasmol.hlp
   . http://www.rasmol.org/donate.shtml
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html
   . http://www.rasmol.org/register.shtml
   . http://www.rasmol.org/software/RasMol_Latest_Windows_Installer.exe
   . http://www.rasmol.org/software/RasMol_Latest.tar.gz
   . http://www.rasmol.org/software/RasMol_Latest_Manual.html
   . http://www.rasmol.org/donate.shtml
   . http://www.rasmol.org/register.shtml
   . http://www.rasmol.org/software/RasMol_2.7.5_Windows_Installer.exe
   . http://www.rasmol.org/software/RasMol_2.7.5.tar.gz
   . http://www.rasmol.org/software/RasMol_2.7.5_Manual.html
   . http://www.rasmol.org/donate.shtml
   . http://www.rasmol.org/register.shtml
   . mailto:jmfernan@ugr.es
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/doc/esrasmol27.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/doc/NOTICE.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/GPL
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/RASLIC
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#Copying
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/INSTALL.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/ChangeLog.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/TODO.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#Introduction
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#CodeAndBinaries
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/ChangeLog/
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/src/
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/src/mac/
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/src/mswin/
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/doc/README.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/data/
   . http://www.bernstein-plus-sons.com/software/RasMol_2.7.4.2
   . http://www.bernstein-plus-sons.com/software/RasMol_2.7.3.1
   . http://blondie.dowling.edu/projects/rasmol
   . http://www.sourceforge.net/projects/openrasmol
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/INSTALL.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/TODO.html
   . http://www.sourceforge.net/projects/openrasmol
   . ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.5.tar.gz
   . http://www.bernstein-plus-sons.com/software/RasMol_2.7.5.tar.gz
   . http://www.sourceforge.net/projects/openrasmol
   . mailto:rasmol@bernstein-plus-sons.com
   . http://www.openrasmol.org/
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#Copying
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#Contents
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/INSTALL.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/ChangeLog.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/TODO.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#Introduction
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html#CodeAndBinaries
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/doc/rasmol.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/doc/esrasmol27.html
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/doc/itrasmol.hlp
   . http://www.rasmol.org/donate.shtml
   . file:///usr/public_ftp/yaya/software/rasmol-2.7.5-17Jul09/README.html
   . http://www.rasmol.org/register.shtml
