RasMol

Category Proteomics>Protein Structure/Modeling Systems/Tools

Abstract RasMol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules.

The program is aimed at display, teaching and generation of publication quality images.

The original program was 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 color schemes and representations.

Currently supported input file formats include:

1) Brookhaven Protein Data Bank (PDB);

2) Tripos’ Alchemy and Sybyl Mol2 formats;

3) Molecular Design Limited’s (MDL) Mol file format (now part of Accelrys, Inc.);

4) Minnesota Supercomputer Center’s (MSC) XMol XYZ format;

5) Chemistry at HARvard Molecular Mechanics (CHARMM) format;

6) Molecular Orbital PACkage (MOPAC) format;

7) CIF format; and

8) Macromolecular Crystallographic Information File (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, and space-filling (CPK models - see below…) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface.

Space-filling models are also called ‘CPK models’ after the chemists Robert Corey, Linus Pauling and Walter Koltun, who pioneered their use.

Atoms may also be labeled with arbitrary text strings. Alternate conformers and multiple Nuclear Magnetic Resonance (NMR) models may be specially colored and identified in atom labels.

Different parts of the molecule may be displayed and colored 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 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 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.

The rendered image may be written out in a variety of formats including both raster and vector PostScript, GIF, PPM, BMP, PICT, Sun raster file or as a MolScript input script or Kinemage (short for kinetic image).

RasMol 2.7.5 Features --

The major changes in RasMol 2.7.5 are:

Support for Structural Biology Extensible Visualization Scripting Language (SBEVSL) movie commands; Support for Lee-Richards surface approximation by contouring pseudo-Gaussian electron densities;

Selection of atoms by proximity to map contours; Coloring of maps by the colors of neighboring atoms; and Significant improvements to the GNU Image Manipulation Program (GIMP) ToolKit (GTK) version by Teemu Ikonen.

RasMol 2.7.4 Features --

The major changes in RasMol 2.7.4 are:

Extended language support; Messages and menus in Bulgarian, Chinese, English, Italian, Japanese, Russian and Spanish are now supported on systems with appropriate fonts;

Support for maps; On systems with sufficient memory, RasMol can read maps in Collaborative Computational Project Number 4 (CCP4) and Crystallographic Binary Files (CBF) map formats and can write maps in CBF map format.

Maps of density from pseudo-Gaussian atoms can be generated. Support is provided for generation of surfaces for Small-Angle X-ray Scattering (SAXS) bead models.

An MS Windows installer was proposed by G. A. Pozhvanov, and re-implemented on the open source base of NSIS-2.21.

A UNIX installer script, ‘rasmol_install.sh’, and a matching script to select an appropriate binary version to run under UNIX; rasmol_run.sh has been added by H. J. Bernstein;

Two new options have been added for the export of Virtual Reality Modeling Language (VRML) images: “rotate” and “mirror”;

Code from 2003 by Vencislav Stanev to export Raster3D scripts from RasMol was integrated with this release, and support for ribbons was also added; and

In order to support builds on newer 64-bit UNIX systems, Nikolay Darakev added code to the build scripts to check the length of long integers and to adjust the builds.

RasMol 2.7.3 Features -

This release includes the base level of code for software rendering of Lee-Richards molecular surfaces, and is intended to provide a stable base for hardware-assisted rendering of molecule surfaces in future releases, and for other changes.

There are major additional changes pending to be applied once this base level is stable, including further molecular surface code and code to apply crystallographic and non-crystallographic symmetry.

System Requirements

Versions of RasMol have 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.

Manufacturer

Manufacturer Web Site RasMol

Price Contact manufacturer.

G6G Abstract Number 20714

G6G Manufacturer Number 104283