One free molecular graphics visualization tool available over the Internet is RasMol, developed by Roger Sayle. RasMol is available for UNIX, VMS, Macintosh and Microsoft Windows (OS/2 and Windows NT). Excellent introductions to RasMol, along with instructions for obtaining and setting up the program, are available at:
* http://www.umass.edu/microbio/rasmol/ (thanks to Eric Martz)
* http://www.pdb.bnl.gov/PPS2/technology/RasMol/rasmol.html. This site is part of the excellent online course “Principles of Protein Structure Using the Internet”
An alternative free visualization tool is the Netscape (TM) 3.01 Plugin called Chime, supplied by:
* MDL Information Systems, Inc. (http://www.mdli.com/chemscape/chime/).
* Additional information about Chime is available at http://www.umass.edu/microbio/chime/index.html. (thanks to Eric Martz again)
A third free visualization tool is WebLab(TM) Viewer, provided by:
* Molecular Simulations, Inc. (http://www.msi.com/viewerlite/).
A fourth free visualization tool is DisMol, created by Peter McCluskey. DisMol is available at:
It is a good deal slower than RasMol (of the 3 parts listed below, only the
fine-motion controller is small enough for a 300 mhz pentium to handle
tolerably well), but has the advantage that once
installed on the server, anyone can use it with a standard Java-enabled
browser without having install new software on their system.
Here are pages which show Drexler’s Simple Molecular Machine Parts via DisMol:
* Simple pump selective for neon
* Fine-motion controller for molecular assembly
* A molecular differential gear
Open Source molecular modeling tools
The following four Web sites were recommended by Peter McCluskey and Eugene Leitl as excellent sources of information on Open Source molecular modeling
This page lists tools (web sites for both commercial and freeware tools) for computational chemists. The tools are grouped in the following categories:
* Charge Fitting Programs
* Crystallography Programs
* Force Fields
* Genetic Algorithms
* Manuals and Guides
* Modeling, Docking, Molecular Design, Drug Design
* Molecular Databases
* Molecular Dynamics & Brownian Dynamics Programs
* Molecular File Format Documentation
* Molecular Mechanics Programs
* Molecular Surface and Volume Computation Programs
* Quantum Chemistry Software
* Quantum Molecular Dynamics, Car-Parrinello Methods
* Simulated Annealing
* Visualization, Animation, and Rendering tools; Molecular editors and Converters
“The Molecular Modelling Toolkit (MMTK) is a program library for molecular modelling applications. Its aim is to provide researchers, especially those working on the development of new simulation and modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling. … MMTK is based on an object-oriented model of molecular systems… developed in and around Python, a high-level object-oriented general-purpose programming language.” This Web site contains in addition to MMTK links to the necessary Python software as well as manuals and papers with applications of MMTK.
This is the Web page for NanoCAD, a freeware nanotech design system based in JavaTM, including source code.
This page lists Linux software of use in chemistry and biology, including commercial, freeware, and GNU General Public License software.