                                   README
                                RasMol 2.7.1

                                  [RasMol]
                    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 (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 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 (C) Herbert J. Bernstein 1998-1999

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 5 July 1999
           Edited by Herbert J. Bernstein and Frances C. Bernstein

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

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

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

                    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
        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

This posting is to announce the release of RasMol version 2.7.1, which makes
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 (6 July 1999), this version has been built for Linuxppc,
SGI, DEC OpenVMS, Mac and IBM PC under Windows 95. Reports of builds and/or
problems on other platforms appreciated. Our thanks to David Atkinson at BU,
Bob Sweet at BNL, Helen Berman at John Westbrook at Rutgers for access to
computers used for some of the compilations for this release.  Additional 
thanks to David Atkinson for contributing the compiled Alpha Dunix binaries.

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

                          Source Code and Binaries

The complete source code and user documentation of RasMol 2.7.1 may be
obtained by anonymous FTP at:

ftp://ftp.bernstein-plus-sons.com/software/RasMol_2.7.1.tar.gz

or on the web at:

http://www.bernstein-plus-sons.com/software/RasMol_2.7.1.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
 SGI (IRIX 5.3):
             RasMol.SGI/IRIX_5.3/rasmol_8BIT.gz          rasmol.hlp.gz
             RasMol.SGI/IRIX_5.3/rasmol_16BIT.gz         rasmol.hlp.gz
             RasMol.SGI/IRIX_5.3/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

 Alpha (OpenVMS 7.1):
             RasMol.DEC/OpenVMS_7.1/rasmol_8bit.exe.gz   rasmol.hlp.gz
             RasMol.DEC/OpenVMS_7.1/rasmol_16bit.exe.gz  rasmol.hlp.gz
             RasMol.DEC/OpenVMS_7.1/rasmol_32bit.exe.gz  rasmol.hlp.gz

 Alpha (Dunix 4.0D):
             RasMol.DEC/Dunix_4.0D/rasmol_8bit.gz        rasmol.hlp.gz
             RasMol.DEC/Dunix_4.0D/rasmol_32bit.gz       rasmol.hlp.gz
 
 VAX (OpenVMS 6.2):
             RasMol.DEC/OpenVMS_6.2/rasmol_8bit.exe.gz   rasmol.hlp.gz
             RasMol.DEC/OpenVMS_6.2/rasmol_16bit.exe.gz  rasmol.hlp.gz
             RasMol.DEC/OpenVMS_6.2/rasmol_32bit.exe.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

 SGI (IRIX 5.3): RasMol.SGI/IRIX_5.3/rasmol_8BIT          rasmol.hlp
                 RasMol.SGI/IRIX_5.3/rasmol_16BIT         rasmol.hlp
                 RasMol.SGI/IRIX_5.3/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

 Alpha (OpenVMS 7.1):
                 RasMol.DEC/OpenVMS_7.1/rasmol_8bit.exe   rasmol.hlp
                 RasMol.DEC/OpenVMS_7.1/rasmol_16bit.exe  rasmol.hlp
                 RasMol.DEC/OpenVMS_7.1/rasmol_32bit.exe  rasmol.hlp
 
 Alpha (Dunix 4.0D):
                 RasMol.DEC/Dunix_4.0D/rasmol_8bit        rasmol.hlp
                 RasMol.DEC/Dunix_4.0D/rasmol_32bit       rasmol.hlp

 VAX (OpenVMS 6.2):
                 RasMol.DEC/OpenVMS_6.2/rasmol_8bit.exe   rasmol.hlp
                 RasMol.DEC/OpenVMS_6.2/rasmol_16bit.exe  rasmol.hlp
                 RasMol.DEC/OpenVMS_6.2/rasmol_32bit.exe  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.

     | 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
