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Rasmol at NERSC
Table of Contents
- Description
- 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.
- Features
- 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.
- Accessing RASMOL
- RASMOL is available on NERSC platforms via the modules facility.
- Documentation
- Links to online local documentation (pdf/html format).
- Additional Resources
- Links to the RASMOL distribution site, supplemental information, a FAQ page.
- Sample Screen Shots
Description
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 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).
Features
- 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.
- More information can be found at the vendor's web site.
Accessing RASMOL
To access rasmol on NERSC platforms, use the modules facility as follows:
% module load rasmol
Documentation
Pdf/postscript Documentation
Local Documentation Downloads: (Use shift left-mouse to download files)
Additional Resources
Sample Screen Shots
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