CCL Home Page
Up Directory CCL README.txt
This software was described on http://www.openrasmol.org/ site.
The actual tar file was retrievd from:


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 

 
Go there to retrieve the latest version.
Here is the original readme file retrieved on 2002.04.26.



     RasMol is a program for molecular graphics visualisation originally
developed by Roger Sayle. This site is provided for the convenience of users
   and software developers of open source versions of RasMol. In order to
    ensure continuing availability of source code and documentation most
 programs and documents on this site are subject to copyright. This does not
   prevent you from using the open-source versions of RasMol, from making
  copies and changes, but prevents the creation of "closed source" versions
 out of the open source versions. Appropriate copyrights and licenses appear
    with the relevant sources and documents. See Copyright and NOTICE for
                  applicable Copyright and other Notices.
  ------------------------------------------------------------------------

                                  Contents

   * IMPORTANT - Copying and Distribution
   * Introduction
   * Software Distributions
   * RasMol Manual
   * Frequently Asked Questions
   * RasMol 2.7 Series History

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

                                Introduction

Welcome to the OpenRasMol web site. This site was established in
mid-September 2000 to provide a home for Open Source versions of RasMol.
RasMol is an important scientific tool for visualisation of molecules
created by Roger Sayle in 1992. RasMol is used by hundreds of thousands of
users world-wide to view macromolecules and to prepare publication-quality
images. Science is best served when the tools we use are fully understood by
those who wield those tools and by those who make used of results obtained
with those tools. When a scientific tool exists as software, access to
source code is an important element in achieving full understanding of that
tool. As our field evolves and new versions of software are required, access
to source allows us to adapt our tools quickly and effectively.

There has always been free access to the source of the main line of RasMol
development. With the creation of the RasMol 2.7 series of releases starting
in 1999, RasMol formally became an open source program. There is some
confusion about the meaning of the phrase "open source". In the early days
of software development, most scientific software source code was freely and
openly shared with a minimum of formalities. These days, it appears that
carefully drawn legal documents are necessary to protect free access to the
source code of scientific software. We are all deeply indebted to Richard
Stallman for showing us how a creative combination of copyrights and
seemingly restrictive licenses could give us truly unfettered freedom to use
programs, to read their source code and to develop new versions. The GNU
project, and the Linux project have shown that an open source approach
works. We do not use the GNU General Public License (the "GPL") for
OpenRasMol, but the OpenRasMol conditions for use have correctly been called
"GPL-like" (see, for example, the Linuxppc port of RasMol 2.7).

You can find a complete explanation of the OpenRasMol conditions in the page
on Copying and Distribution. If you are a user of OpenRasMol programs, you
will find that the copyrights and notices ask little more of you than that
you avoid mistakes by others by keeping the notices with copies, display
scientific integrity by citing your sources properly and treating this like
other shared scientific developments by not inferring a warranty. If you are
a software developer and wish to incorporate what you find here into new
code, or to pick up bits and pieces and used them in another context, the
situation becomes more complex. Read the copyrights and notices carefully.
You will find that they are "infectious". Whatever you make from our Open
Source code must itself be offered as Open Source code. In addition, in
order to allow users to understand what has changed and to ensure orderly
development you have to describe your changes.

There is a lot still to be done before this site is fully functional. Many
links and features need to be added. With your help, with your comments,
suggestions and corrections, and with contributions of new Open Source
RasMol code and documentation, hopefully this site will evolve into an
increasingly useful tool for the community.

     -- H. J. Bernstein

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

                           Software Distributions

   * RasMol Features
   * RasMol -- prior stable release (RasMol 2.7.1)
        o RasMol 2.7.1 Features
   * RasMol -- latest stable release (RasMol 2.7.1.1)
        o RasMol 2.7.1.1 Features
   * RasMol -- prior test version (RasMol 2.7.2)
        o RasMol 2.7.2 Features
   * RasMol -- best test version (RasMol 2.7.2.1)
        o RasMol 2.7.2.1 Features
   * RasMol -- test version of patches to support zlib under RasMol 2.7.2.1
        o RasMol zlib support status

   * ***NEW*** RasTop -- latest stable release (RasTop 2.0)
        o RasTop 2.0 Features
        o Source code patches for RasTop 2.0
   * RasTop -- prior releases
        o RasTop 1.3.1 Features
        o RasTop 1.3 Features

RasMol Features

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. RasMol runs
on wide range of architectures and operating systems including Microsoft
Windows, Apple Macintosh, UNIX and VMS systems. UNIX and VMS versions
require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The X
Windows version of RasMol provides optional support for a hardware dials box
and accelerated shared memory communication (via the XInput and MIT-SHM
extensions) if available on the current X Server.

The program reads in a molecule coordinate file and interactively displays
the molecule on the screen in a variety of colour schemes and molecule
representations. Currently available representations include depth-cued
wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick,
solid and strand biomolecular ribbons, atom labels and dot surfaces.

The X Windows version of RasMol provides optional support for a hardware
dials box and accelerated shared memory communication (via the XInput and
MIT-SHM extensions) if available on the current X Server.

The program reads in molecular coordinate files and interactively displays
the molecule on the screen in a variety of representations and colour
schemes. Supported input file formats include Protein Data Bank (PDB),
Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design
Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ
(XMol) format, CHARMm format, CIF format and mmCIF format files. If
connectivity information is not contained in the file this is calculated
automatically. The loaded molecule can be shown as wireframe bonds, cylinder
'Dreiding' stick bonds, alpha-carbon trace, space-filling (CPK) spheres,
macromolecular ribbons (either smooth shaded solid ribbons or parallel
strands), hydrogen bonding and dot surface representations. 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 represented and coloured
independently of the rest of the molecule or displayed in several
representations simultaneously. The displayed molecule may be rotated,
translated, zoomed and z-clipped (slabbed) interactively using either the
mouse, the scroll bars, the command line or an attached dial box. RasMol can
read a prepared list of commands from a 'script' file (or via inter-process
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 either raster or vector PostScript, GIF,
PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage.

The RasMol help facility can be accessed by typing "help " or "help
 " from the command line. A complete list of RasMol
commands may be displayed by typing "help commands". A single question mark
may also be used to abbreviate the keyword "help". Please type "help
notices" for important notices.

Released by R. Sayle (RasMol 2.1) 1993

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

RasMol 2.7.1 Features

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 centring logic.

Released by H. J. Bernstein, 22 June 1999

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

RasMol 2.7.1.1 Features

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. Our
     thanks to Fernando Gabriel Ranea for most of the translations.
   * Upgrade of some of the Windows printer logic
   * Correction of coordinate handling for Mol2 and XYZ coordinates
   * Fix to the parsing of D2O.

Released by H. J. Bernstein, 21 January 2001

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

RasMol 2.7.2 Features

The preliminary release of RasMol 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 colours 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.

Released by H. J. Bernstein, 28 August 2000
  ------------------------------------------------------------------------

RasMol 2.7.2.1 Features

The release of RasMol 2.7.2.1 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.

This release should hopefully represent a move toward stability for the
2.7.2 versions. However, in order to allow for prompt release of the French
and Italian versions, some pending corrections have not yet been integrated.
Comments and suggestions appreciated.

Released by H. J. Bernstein, 14 April 2001
  ------------------------------------------------------------------------

RasMol 2.7.2.1 zlib patches

The Unix version of RasMol supports decompression of compressed data files
using pipes. Mamoru Yamanishi has prepared modifications for RasMol 2.7.2.1
to support use of decompression using the zlib (http://www.gzip.org/zlib)
library, which should allow decompression of compressed data files on
non-Unix platforms. These new modifications are being studied for inclusion
in a future RasMol standard release for use on systems for which a pipe to a
standard decompression utility is not practical to use. The source code mods
to RasMol 2.7.2.1 for use of zlib under Mac OS are available for testing.

Released by Mamoru Yamanishi yama@biotech.okayama-u.ac.jp, 13 July 2001
  ------------------------------------------------------------------------

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

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

RasTop 1.3.1 Features

This is a minor update with modifications concerning mainly correction of
bugs reported for the 1.3 version. The software is now supported under
Windows 2000 operating system. The software seems also stable under Windows
ME. A release for 8-bit monitors is also available (although never tested on
a true 256 colors monitor). A few systems are missing an updated version of
the mfc42.dll file which is also available, but requires separate
installation.

Operationally, there are very few changes. Maybe the most interesting for
rasmol is the use of white color for carbon atoms when there are no hydrogen
on the molecule on opening. The squareroot calculations for drawing ribbons
at large zoom have been corrected.

Released by P. Valadon, 25 March 2001

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

RasTop 2.0 Features

RasTop 2.0 is a user-friendly graphical interface build on top of RasMol
(version 2.7.2.1) available for Windows platforms. This is a major update
over the 1.3.1 version. The interface now accepts multiple molecules. It has
high color resolution and improvement of the rendering (depth queuing,
multidirectional headlight, new cylinder code, better ribbons). The Richards
- Connolly surfaces are now complete. A script can be started automatically
on molecule opening.

Comments, suggestions, and bug reports will be extremely appreciated. The
immediate goal is to obtain stable multiple molecule environment and
compatibility with recent versions of Windows.

Released by P. Valadon, 20 January 2002

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

      | Copying and Distribution | Contents | Software Distributions |
 | RasMol Manual | Frequently Asked Questions | RasMol 2.7 Series History |
                                 OpenRasMol|

www.OpenRasMol.org

  ------------------------------------------------------------------------
  The OpenRasMol site is provided courtesy of Bernstein + Sons, Information
                            Systems Consultants.
Portions  Copyright Herbert J. Bernstein 2000. All Rights Reserved. Other
copyrights apply. License to copy most pages on this site will be granted if
certain open source and other conditions are adhered to. See
http://www.OpenRasMol.org/Copyright.html. To request permission to copy any
elements from our pages, or to send comments about our pages, please write
to webmaster@OpenRasMol.org. If you establish a link to one of our pages,
please let us know! Updated 27 January 2002
Modified: Fri Apr 26 21:10:14 2002 GMT
Page accessed 4970 times since Fri Apr 26 21:15:33 2002 GMT