RasMol-2.6b2: description + notes
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RasMol 2.6
Molecular Graphics Visualisation tool.
Roger Sayle
Biomolecular Structures Group
Glaxo Wellcome Research & Development
Stevenage, Hertfordshire, UK.
September 1995
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 and CHARMm 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. 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.
The source code is public domain and freely distributable provided that
the original author is suitably acknowledged. The complete source code and
user documentation may be obtained by anonymous FTP from ftp.dcs.ed.ac.uk
[129.215.160.5] in the directory /pub/rasmol. The source code, documentation
and Microsoft Windows executables are stored in several files appropriate
for the receiving operating system. Please read the "README" file in the
distribution directory. UNIX and VAX systems should retreive either
RasMol2.tar.Z, RasMol2.tar.gz. Apple Mac users should retrieve RasMac.sit.hqx.
Microsoft Windows users should retrieve RasWin.zip and optionally the Visual
Basic package RasMenu.zip. All these files include source code, on-line help,
user manual and reference card. RasMac.sit.hqx, RasWin.zip and RasMenu.zip
also contain executables for the required platform. 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 the package may be directed
to the author at "rasmol@ggr.co.uk".
Roger
--
--
Roger Sayle INTERNET: ras32425@ggr.co.uk
Glaxo Wellcome Medicines Research Centre, rasmol@ggr.co.uk
Gunnels Wood Road, Stevenage, Tel: +44 (0)1438 763246 (direct line)
Hertfordshire, SG1 2NY, U.K. Fax: +44 (0)1438 763082
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