Back to TABLE OF CONTENTS  Introductions to: RasMol v2.5 HTML & 2.6 Versions
RasMol v2.5
A Molecular Visualisation Program
Roger Sayle
Glaxo Wellcome Research and Development
Stevenage, Hertfordshire, U.K.

Introduction to v2.5 Manual
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 SGI, sun4, sun3, sun386i, DEC, HP and E&S workstations, DEC Alpha (OSF/1, Open VMS and Windows NT), IBM RS/6000, Cray, Sequent, VAX VMS (under DEC windows), IBM PC (under Microsoft Windows, Windows NT, OS/2, Linux, BSD386 and *BSD), Apple Macintosh and PowerMac. 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 communication (via the XInput and MIT- SHM extensions) if available on the current X Server.
The program reads in molecular co-ordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Brookhaven Protein Databank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Centre's (MSC) XYZ (XMol) format and CHARMm 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. 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 a Kinemage.
RasMol has been developed at the University of Edinburgh's Biocomputing Research Unit and the BioMolecular Structure Department, Glaxo Research and Development, Greenford, U.K.
If you have any comments, questions, suggestions or complaints please do not hesitate to contact the author:

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