Free Molecular Visualization Software

Other than RasMol

Viewing/rendering: molecular visualizers
Conversion/manipulation of atomic coordinate data files
Animation/movie making
Software lists at other sites

Viewers/renderers/visualizers

Chemscape Chime from MDL Information Systems, Inc., allows rotating a molecular image within a Netscape page. Multiple molecules can be displayed within a single web page, unlike helper applications (such as RasMol) which display each molecule in a separate window. Chime also supports scripts (using a superset of the RasMol scripting language). See the UMass Chime Resources page for the latest and greatest educational Chime scripts.

MAGE's animation of deoxy to carbonmonoxy transition of heme in hemoglobin (Protour8.kin).
After 25 cycles, animation will stop. Reload to reanimate.
MAGE (Windows, Mac, unix) offers over a thousand excellent tutorials on molecular structures in the form of kinemages! MAGE, by David Richardson, is the freeware which first brought powerful macromolecular visualization to personal computers. Here is a more detailed overview comparing MAGE with RasMol.
Swiss-PdbViewer program by Nicolas Guex and Manuel C. Pietsch. This program runs on Macintosh or Windows NT/95 (but not Windows 3.1x). You can overlay and align multiple structures, mutate amino acids (the best rotamer of the new AA is found automatically), and dynamically find/display hydrogen bonds. Upgraded to version 2.0 March, 1996 (first Windows version; Mac version now supports Quickdraw3D).
MolMol (Win95, unix) makes publication quality images including surfaces, and has a graphical user interface with menus, dialog boxes and on-line help, including a hypertext manual and tutorial. Especially good support for multi-model NMR files. Supports limited modeling (addition or removal of atoms/bonds, and rotation around dihedral angles). Here is a Gallery of MolMol Images.
Cn3D (Read as See in 3D) is a superb new free viewer from the National Center for Biotechnology Information. It uses "cleaned-up" PDB files converted to ASN.1 format available thru WWW Entrez, also available directly within Cn3D which will itself query the Entrez database. Considerable effort has been applied to the ASN.1 data files to resolve ambiguities present in the PDB format and remove errors present in some PDB files. See the on-line article by Hogue et al. for an explanation. Cn3D is more intelligent than RasMol -- for example, it provides a more informative first image of a structure.
WebLab from Molecular Simulations, Inc. is free and runs on Windows and Macintoshes, and is in part derived from RasMol. It can represent alpha helices as cylinders, can add missing hydrogen atoms, and can rotate residues around a bond (torsion). Excellent for selecting (including by mouse clicking) a subset of atoms and saving them to a separate file. MSI offers nice prepackaged sets of examples of various types of molecular structures (mostly readable only in WebLab, though). WebLab is highly recommended!
The Molecule to Image Converter Engine by Jozsef Ferincz is an amazing web form which allows you to submit a PDB file URL, and get back a RasMol image!
MolView and MolView Lite are described by their author, Thomas J. Smith, as follows. Freeware programs written for the Mac. The user cannot only display proteins in all of the various ways but can also analyze them (e.g. distances, Ramachandran plots, Edmunson wheels, hydrophathy plots, 3D structure alignments). Ribbon drawings can be drawn in many different ways - all controlled by graphical buttons. Subsets of structures can be written out to 'MOL files' to be read in at a later time. While there is more flexibility in display options than other programs, the interface is entirely graphically based and not script driven. In contrast to most other programs, the output images are mostly kept as object-oriented PICT files for very high quality prints. Finally, the user can also output 3 different kinds of QuickTime movies, line DXF files, and Apple's new 3DMF files for interactively rendered ball&stick, ribbon, space filling, line, and 'tube' models.
LinusLite is a free test version of a forthcoming enhanced version of the commercial viewer MacMolecule. These programs run only on the Macintosh, and require a special atomic coordinate data file format, generated from PDB files with a free translator provided.
Midas+ isn't free from UCSF but an academic license costs only $350. It is very powerful and runs on Silicon Graphics, DEC Alpha AXP, and NeXT workstations.
ChemDraw & Chem3D, free demo software from CambridgeSoft Corp., which also provides a web-searchable database of molecules. (Windows, Mac, unix)

Animation/movie making
WPDB (Windows Protein Data Base)
MovieMol makes ball-and-stick animations of molecular structures, and runs on PC DOS, IBM RISC/6000, and SGI workstations. It is free to academic researchers.
Free Molecular Animations using Animation Works show off alpha helix, beta sheet, DNA, tRNA, homeoboxes, and DNA polymerase.
VMD (Visual Molecular Dynamics) runs on Silicon Graphics workstations (IRIX 5.x). This sophisticated package can produce virtual reality 3D, show molecular dynamics simulations, and has a script language complete with loops, variables, conditional branching, and subroutines. It comes complete with C++ source code from the Theoretical Biophysics Group of the Beckman Institute at the Univ Illinois Urbana-Champaign.

Conversion/manipulation of atomic coordinate data files
Babel by Pat Walters and Matt Stahl (U AZ, Tuscon) interconverts many atomic coordinate data file formats (e.g. Alchemy to PDB or vice versa). It runs on Windows, Macs, and unix systems. It can also assign hybridization, bond order, and connectivity when these elements are not present in the input file. If you just need a few quick conversions, Jozsef Ferincz has provided an amazing web form you can fill out -- the converted file will appear in your browser and can be saved to disk! It is the Molecular Modeling Interconverter Engine.
Hingefind is an X-PLOR script by Willy Wriggers which identifies domain movements in proteins. It generates output files which can be visualized with standard software.
Computational Center for Macromolecular Structures, CCMS, at the San Diego Supercomputer Center. Here you can get free programs including SHAPE (analysis of molecular surfaces), FLEX (molecular animations), PDBtool (browser), XTALVIEW (X-ray crystal structure solver). These are mostly for unix/workstations/xwindows systems.
MolGen (Windows, OS/2, Sun) computes molecular structures. Free demo for up to 100 atoms. University of Bayreuth, Germany.
PDBTools, a small package of home-made C programs for extracting subsets of PDB files or combining PDB files.

Software lists at other sites
The US NIH Molecular Modeling group provides a very comprehensive listing of software (free and commercial).
The Institute for Molecular Virology at the Univ Wisconsin maintains an annotated list of molecular visualization software.
The Protein Data Bank lists some free software tools for advanced protein structurists.
A comprehensive software list is provided by Yves Epelboin at the SINCris server of the Paris Minerology and Crystallograpy Laboratory.

Back to Free Molecular Visualization Resources Other than RasMol

This page is maintained by emartz@microbio.umass.edu

Free Molecular Visualization Software

Other than RasMol

Viewers/renderers/visualizers

Animation/movie making

Conversion/manipulation of atomic coordinate data files

Software lists at other sites