Posted July 20, 2013 by Dr. Henri Montandon in brain experiments

Good ol’ RasMol: Molecular modeling for the masses










Chemical effects on the brain are both fascinating and necessary for survival. Endogenous neuromodulators and neurotransmitters and their receptors are switches which increase, decrease or stabilize brain’s functioning. Exogenous narcotics, intoxicants, anesthetics, entheogens, etc. have throughout human history played prominent roles in medicine, recreation and spirituality.

Regarding brain scientists, scale is an important taxonomic family. Theories tend to be scale-specific from Ångstrom-scale chemical models to internet-scale conjectures suggesting new guesses for how brains develop and evolve.

Ångstrom scale modeling programs for use by neuroscientists are fun because we have such great visualization toys to play with. RasMol was one of the first and remains ever true to its GNU heritage.

From RasMol README:

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 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 colour schemes and representations. 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.

What can RasMol do for you?
























From RasMol Quick Start:

Imagine being able to generate such images of your favorite molecules, and then rotate them, or view them in stereo, to comprehend their 3D structure! RasMol allows you to explore the structure of a molecule by “getting into it and climbing around”. RasMol works well both for small organic molecules and for large ones, such as proteins, DNA, and RNA.








Dr. Henri Montandon