Where does one get "molecules" for RasMol to display?

In order to display a molecule, RasMol needs an atomic coordinate file for that molecule. Atomic coordinate files are often called "PDB" files because the Protein Data Bank format is one of the most widely used. Sources of PDB files are listed below, grouped for


See the bottom of this page for whole virus particles and lipid bilayers!

The primary repository for all published protein and nucleic acid (macromolecular) 3D structures is the Protein Data Bank, These data files are in PDB format.

We recommend that you download PDB files for molecules of interest, saving copies to your hard disk. You can then open them for exploration in RasMol whenever you wish, without a network connection.

Find, View, Download Macromolecules
from the Protein Data Bank
with PDB Lite

The US National Institutes of Health (NIH) provides Molecules R Us, an especially user-friendly search tool for the Brookhaven PDB collection, and a tabular, hypertext classification in their PDB at a Glance. The National Center for Biotechnology Information (NCBI) of NIH provides WWW-Entrez, a powerful 3D and structural relationship database. SCOP (Structural Classification Of Proteins) offers an on-line search from the MRC Lab of Molecular Biology & Centre for Protein Engineering, Cambridge UK. These and several other major sources of atomic coordinate files are listed in a comprehensive index at the US NIH Molecular Modeling home page. Click on Research Tools on the Network in the left column. Another user-friendly interface in Europe is Swiss-3D-Image.

For DNA and RNA PDB files categorized according to structure (A-, B-, Z-DNA, anomalies, intercalations, complexes, etc.), go to the Atlas of Nucleic Acid-Containing Structures at the Nucleic Acid Database at Rutgers U.

David Marcey, Kenyon College, Gambier OH US, provides an illustrated selection of protein and nucleic acid PDB's.

The Protein Motions Database indexes PDB's showing different conformations of the same molecule.

Supply your own sequence and get back a theoretical PDB model, free! This amazing service is available at Swiss-Model.


The KLOTHO database from Washington University, St. Louis MO, provides a searchable database of over 400 micromolecules of general biochemical interest.

This and several other major sources of atomic coordinate files for micromolecules are listed at the US NIH Molecular Modeling home page. Click on Small Molecule Database Access in the right column.

Dave Woodcock at the Okanagan University College Chemistry Dept (BC CA) provides over 500 PDB files nicely categorized, including aspartame, butane in 3 conformations, caffeine, epinephrine, ibuprofen, LSD, Socrates' hemlock poison, taxol, TNT, valium, and many examples of simple organic compounds.

Tokyo University of Pharmacy and Life Science's 3D Molecular Modeling Homepage (from Akira Dobashi's group) offers PDB files for thousands of pharmaceutical compounds. The PDB's include double bonds. This site also has molecular dynamic animations of all these molecules!

Additional micromolecular structures are available from the MultiCHEM facility at the University of California, Berkeley. Look towards the bottom of their RasMol page for their Smells database of odorous micromolecules.

CORINA is a fabulous program which will generate a theoretical 3D structure for the micromolecule of your choice, free! (for the first 1000).

If you don't find the micromolecule you want in the above collections, 2,500 more are available via ChemFinder. These are not in RasMol viewable format but can be viewed with free software provided by CambridgeSoft Corp. and/or converted to PDB.

Noncovalent assemblies of molecules

Lipid Bilayer Membranes.

Whole Virus Particles

The University of Wisconsin Institute for Molecular Virology Robert M. Bock Laboratories Virus Visualization page provides a PDB file for a rhinovirus capsid (all 48,000 alpha carbons!). This gives even RasMol reason to pause!

Inorganic Crystal Structures

Lattice Structures for inorganic molecules are available from the Complex Systems Theory Branch, Code 6690 of the Naval Research Laboratory. Their page "currently contains links to 71 structures in 35 of the 230 space groups"(as of 10/22/98). Selected examples of these can be viewed at through Chime at Andrew Maverick's crystal page.

If you know of other sources of RasMol-displayable atomic coordinate files, please tell emartz@microbio.umass.edu so they can be included here.

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