                                   README
                               RasMol 2.7.1.1

                                   RasMol
                   Molecular Graphics Visualisation Tool
                              21 January 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 (C) Roger Sayle 1992-1999

                     and Based on Mods by Arne Mueller
                          Version 2.6x1, May 1998
                      Copyright (C) Arne Mueller 1998

         Version 2.7.0, 2.7.1, 2.7.1.1 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, 2.7.1.1 January 2001
                Copyright (C) Herbert J. Bernstein 1998-2001

    Translations of most of the RasMol messages into Spanish contributed
       by Fernando Gabriel Ranea (Laboratorio de Micología, Museo de
     Farmacobotánica, Facultad de Farmacia y Bioquímica. Universidad de
                  Buenos Aires (davinci@dinamica.com.ar)).

   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.

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

              Translation of RasMol 2.7.1 Manual into Spanish

   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.
     _________________________________________________________________

                   Test Version of Next Release Available

   RasMol 2.7.1.1 is an interim release for testing of the integration of
   multilingual capabilities into RasMol. These same mods will then be
   integrated with pending mods, and with the basic structure of RasMol
   2.7.2 to create RasMol 2.7.2.1.

   A preliminary release of RasMol 2.7.2 (without the multilingual
   capabilities) is available at:

          http://www.bernstein-plus-sons.com/software/RasMol_2.7.2

      THIS IS A PRELIMINARY RELEASE INVOLVING EXTENSIVE MODIFICATIONS
                       ***** USE WITH CAUTION ******
     _________________________________________________________________

                            RasTop 1.3 Available

   RasTop by P. Valadon is a graphical interface to RasMol adapted for
   Windows platform, i.e. RasTop is a GUI front end for RasWin.

     RasTop -- GUI front end for RasWin (RasTop 1.3)
     * RasTop 1.3 Features
     _________________________________________________________________

                    IMPORTANT - Copying and Distribution

   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.
     _________________________________________________________________

                                  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

   This posting is to announce the release of RasMol version 2.7.1.1,
   which makes 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 is 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.

   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 (29 January 2001), this version has been built for
   i586 Mandrake 7.2 Linux, Mac, IBM PC under Windows 95/98, and SGI
   IRIX 6.4. Reports of builds and/or problems on other platforms
   appreciated.
     _________________________________________________________________

                          Source Code and Binaries

   The complete source code and user documentation of RasMol 2.7.1.1 may
   be obtained by anonymous FTP at:

   ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.1.1.tar.gz

   or on the web at:

   http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.1.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!!!

   System    Binary                                  Help Files
   Linux (Mandrake 7.2, i586):
             RasMol.LINUX/Mandrake_7.2/i586/rasmol_8BIT.gz 
                                                     rasmol.hlp.gz
             RasMol.LINUX/Mandrake_7.2/i586/rasmol_16BIT.gz
                                                     rasmol.hlp.gz
             RasMol.LINUX/Mandrake_7.2/i586/rasmol_32BIT.gz
                                                     rasmol.hlp.gz

   SGI (IRIX 6.4):
             RasMol.SGI/IRIX_6.4/rasmol_8BIT.gz      rasmol.hlp.gz
             RasMol.SGI/IRIX_6.4/rasmol_16BIT.gz     rasmol.hlp.gz
             RasMol.SGI/IRIX_6.4/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 via the HTML web page only:

   System    Binary                                  Help Files
   Linux (Mandrake 7.2, i586): 
             RasMol.LINUX/Mandrake_7.2/i586/rasmol_8BIT
                                                     rasmol.hlp
             RasMol.LINUX/Mandrake_7.2/i586/rasmol_16BIT 
                                                     rasmol.hlp
             RasMol.LINUX/Mandrake_7.2/i586/rasmol_32BIT 
                                                     rasmol.hlp
   SGI (IRIX 6.4): 
             RasMol.SGI/IRIX_6.4/rasmol_8BIT         rasmol.hlp
             RasMol.SGI/IRIX_6.4/rasmol_16BIT        rasmol.hlp
             RasMol.SGI/IRIX_6.4/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.
     _________________________________________________________________

    RasTop 1.3 Features

   RasTop is a graphical interface to RasMol adapted for Windows
   platform, i.e. RasTop is a GUI front end for RasWin.

   RasTop offers a user-friendly graphical interface around "RasMol
   molecular engine". No more typing on the command line; each command in
   the menu generates its own script that is transferred to RasMol.
   RasTop has numerous extensions to handle atom selections: addition and
   subtraction of atoms, groups, or chains, selection on screen with a
   lasso, ability to go back to the previous selection, copying to and
   pasting selections from the clipboard, new set operations such as
   inverse, extraction, summation, subtraction, and exclusion, and
   finally full saving of all user-defined atom sets under an extended
   script format called RSM script.

   During its development, a few new capabilities were added: back
   clipping, 32-bit output under Windows, full centring command either on
   a selected atom or to the origin, variation of depthcue in slab mode,
   and a colouring command, shadepower, which generates new metal-like
   surfaces.

   RasTop allows several molecules to be opened at the same time (on
   different windows) and provides limited editing of the molecular file.

   RasTop 1.3, like RasMol 2.7.1, contains a lot of new code. Under its
   current version, RasTop 1.3 has been extensively tested with molecular
   files in pdb format and showed good stability. Nevertheless you should
   be careful in testing other formats.

   Released by P. Valadon, 27 August 2000
     _________________________________________________________________

     | OpenRasMol | Copying and Distribution | Contents | Installation
                               Instructions |
    | Changes | Things To Do | Introduction | Source Code and Binaries |
   | RasMol Manual | Spanish Translation of RasMol Manual| Release README
                                     |
     _________________________________________________________________

   Updated 29 January 2001.
   Herbert J. Bernstein
   Bernstein + Sons, 5 Brewster Lane, Bellport, NY 11713-2803, USA
   yaya@bernstein-plus-sons.com
   +1-631-286-1339
