RasMol General Description

The above image is of ribonuclease with the atoms colored according to temperature factor value. This is done with one click in RasMol.

RasMol was written by Roger Sayle, BioMolecular Structures Group, Glaxo Research & Development, Greenford, Middlesex, UK. 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 displays on the NCD Xterm windows!

• 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 (Dreiding) stick bonds, alpha-carbon trace, spacefillin (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 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 urrent 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.

To get started, type:

setup rasmol

or

source /srv/local/setup/rasmol.set

Then type:

rasmol

You will give line commands in the UNIX window and select options in the RasMol window.

Online documentation is available as a web page or an Adobe PDF, and a hard copy (v 2.6) is in the core area. There is also a RASMOL Home Page for version 2.7 and version 2.6

Please note - If you publish a figure using this program cite the following: