| Supplied Information: |
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 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 PDB, Tripos' Alchemy and Sybyl Mol2, MDL Mol , MSC XMol XYZ and CHARMm. The loaded molecule may be shown as wireframe, cylinder (Dreiding) 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. 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. The rendered image may be written out in a variety of formats. RasMol will run on a wide range of architectures and systems. Download from http://www.umass.edu/microbio/rasmol/, source available from ftp://ftp.dcs.ed.ac.uk/pub/rasmol/ |
| Review: |
RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program was developed by Roger Sayle [ras32425@ggr.co.uk] at Glaxo and the University of Edinburgh for the display, and generation of publication quality images in teaching and research.
The program reads in a molecular coordinate file in various formats including Brookhaven Protein Databank (.pdb) files, Alchemy and Sybyl Mol2 formats, MDL (.mol) files, XMol (.xyz) files and CHARMm format files. If connectivity information is not contained in the file this is calculated automatically. Note that RasMol2 is designed to only display/manipulate one molecule at a time.
The user is able to interactively control the display mode (eg, wireframe bonds, cylinder 'Dreiding' stick bonds, alpha-carbon trace, etc), rotation, and other aspects of the image by use of mouse-driven menus. Commands controlling these basic options can also be typed into a command window. More complicated options (changing the background colour, identifying the hydrogen bonds, reporting the number of helices, strands and turns, etc) are accessed only through the command window.
The finished image may be saved as PostScript, GIF, PPM, BMP, PICT, Sun rasterfile, MolScript input script or Kinemage, or copy-and-pasted to other programs.
All the commands are described in a user manual and ready-reference card, both supplied as Word documents, or accessed via the WWW [ftp://ftp.dcs.ed.ac.uk/pub/rasmol/]. The manual includes a comprehensive list of references. There is also an interactive help facility, accessed from the command window by typing ģhelpī.
RasMol2 runs on SGI, sun4, sun3, sun386i, DEC, HP and E&S workstations, DEC Alpha, IBM RS/6000, Cray, Sequent, VAX VMS, IBM PC (and compatibles), Apple Macintosh and PowerMac. RasMol2 is used at many universities in Australia and overseas [see (eg) the WWW-based Protein Structure course at http://www.cryst.bbk.ac.uk/PPS2/].
RasMol2 is an outstanding program. RasMol2 is provided free to academic users via the WWW [ftp://ftp.dcs.ed.ac.uk/pub/rasmol/]. ChemScape Chime, which is the WWW browser plug-in version of RasMol2, is available (also free!) from MDL Information systems [http://www.mdli.com/chemscape/chime].
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