In the past few years a new molecular machine design tool, NanoEngineer, has emerged as the best software package available for the design of molecular machine systems of the type that you see on this website. Designs that previously took days to design and model can now be developed in minutes or hours. It’s free and OpenSource.
Dr. Drexler has made his molecular machine parts designs available in the form of files that specify the coordinates in three-dimensional space of each atom in the design. Such atomic coordinate files can be formatted in a number of different file types (chemical MIME types). Information about chemical MIME types can be found at:
- Wikipedia article on chemical file formats.
The files of Dr. Drexler’s designs are in the PDB, or protein data bank, format. This chemical MIME type is often used for large molecules, especially proteins. The RCSB Protein Data Bank currently has nearly 6000 atomic coordinate files, mostly of protein molecules.
To view the structures that are encoded by these atomic coordinate files (which have the extension .pdb), and to be able to manipulate the images to view the molecules from various perspectives, requires a molecular graphics visualization tool. Without a proper tool, the PDB file will be read as a text file that lists each atom and its numerical coordinates in 3-D space.
To directly visualize the molecule when the link to a PDB file is activated, two things are necessary:
- The server sending the file must be configured to tell the browser that the file is a pdb file, a chemical MIME type. Our server is configured to send this MIME type.
- The browser must have a molecular graphics visualization tool that can recognize that MIME type (in this case, a pdb file) as either a helper application or a plug-in. (See the appropriate menu for your browser; for example, in Netscape a plug-in is placed in the Plug-ins folder and helper applications are selected under the Options menu: General Preferences: Helpers)
If either of the above two requirements is lacking, the file must be saved to disk and then opened with the appropriate visualization tool.
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
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.