Free Molecular Modeling Software
RasMol
Chime is based on an older molecular modeling program called RasMol
written by Roger Sayle. Chime has inherited many features from its parent program.
There are things that you can do with RasMol that you can't do with Chime, and
vice-versa. Like Chime, it is free.
Download
The original Rasmol is command-line driven. Marco Molinari of UC Berkeley has
developed UCB-Rasmol
which adds a graphical interface for model manipulation tools. UCB-Rasmol can
also load up to five molecules at a time and move them independently.
Download
ChemOffice
This commercial molecular modeling package is available from CambridgeSoft Corporation.
The free version is called CS
ChemOffice Net. Although limited in functionality, this package includes viewers
that can be used to view both 2D and 3D molecular structures.
Download
How to Find Sites Using Chime
Chime
Resources by Eric Martz
This is the premier site for anyone wanting to learn how to use Chime and Rasmol.
In addition to maintaining this site and the Rasmol
Home Page, Martz has developed several Chime-based biochemistry tutorials.
Martz has also compiled the comprehensive World
Index to Educational BioMolecular Structure Tutorials in Chime and Rasmol
list. It is the most complete directory of biological Chime resources.
Chemscape
Chime Examples Page
The developers of Chime, MDL Information Services,
offer this excellent page with links to many Chime-based chemistry resources on
the World Wide Web. In addition, there is a Chime
Primer on writing your own web pages with Chime models. Because Eric Martz'
index mentioned above contains only biological chemistry references, the Chemscape
Chime Examples Page is the best source of physical and inorganic chemistry Chime
resources.
Others
Lessons using Chime in an organic chemistry course can be found at the
Colby
College Chemistry Department.
A course in Medical Biochemistry at the University of Kansas makes extensive
use of Chime and molecular models in several
tutorials available online.
Sources of Models
Chime can open several types of molecular model files. The two most common
of these formats are PDB files, which have a suffix of .pdb, and MDL
molfiles, which have a suffix of .mol. Already built PDB and molfiles
can be found at many sites on the World Wide Web. Here are a few sites that
we have found to be useful.
Protein
Data Bank (PDB)
The Brookhaven National Laboratory's Protein Data Bank contains over 5000 NMR,
crystallographic, and theoretical macromolecular structure files. These files
are accessible via the PDB
Browser.
European
Bioinformatics Institute
The European Bioinformatics Institute (EBI) site contains a large collection
of crystal macromolecule structures. There is also a UK
mirror of the Brookhaven PDB molecule browser.
CS
ChemFinder
CambridgeSoft's Chemfinder has a great database of small organic and inorganic
molecules, which offers structures, physical constants, and web links for each
compound. Unfortunately structures are only available in the 2D CS ChemDraw
format. Several commercial 3D modeling programs can convert these 2D files into
PDB and molfiles, but we do not know of a free program that does this.
Klotho
Biochemical Compounds Declarative Database
Klotho offers over 400 biological models in PDB format. It is one of the few
relatively large sources of smaller PDB molecules that we have found on the
web. Klotho is maintained by the Institute for Biomedical Computing at Washington
University.
Got a link or resource to recommend? Please send it to haungar@cruzio.com
