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
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!
David Richardson, is the freeware which first brought powerful
macromolecular visualization to personal computers. Here
is a more detailed overview comparing
MAGE with RasMol.
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.
(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
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
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.
is a free test version of a forthcoming enhanced version of the
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)
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
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.
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.
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
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.