Visualization

Visualizing the structures of proteins and nucleic acids requires that the cartesian coordinates of the atoms in the molecule be defined. The coordinates are most often determined using X-ray crystallography or NMR, though models based on sequence homology may be useful for some purposes.

General Resources

Databases

Macromolecules

Research Collaboratory for Structural Bioinformatics (RCSB) - Protein Data Bank
The Nucleic Acid Database
The Molecular Modeling Database at NCBI
BioMagResBank - Repository for Data on Proteins, Peptides, and Nucleic Acids from NMR Spectroscopy
IMB Jena Image Library of Biological Macromolecules

Small Molecules

Viewers
Several programs, both freeware and commercial, are available for structure visualization. Below is a listing of some of these programs.

VMD: Visual Molecular Dynamics, which is being developed at the University of Illinois, is available for UNIX, MacOSX, and Windows.

Pymol: An open source product that includes an embedded Python interpreter. Runs on UNIX, MacOSX, Windows.

Deep View/Swiss-PDBViewer: This program is freeware; versions are available for Macintosh and Windows. It can be used for modeling, visualization and comparison of protein structures. An excellent tutorial is available.

Rasmol:This program is freeware; versions are available for Macintosh, Windows, and UNIX platforms. It can be used as a helper application with your Web browser.

Chime:This program is based on Rasmol and also comes in versions for Macintosh, Windows, and UNIX. It is used as a Plug-in with your Web browser.

MidasPlus:This program, which runs under UNIX, is licensed from the Computer Graphics Laboratory at the University of California at San Francisco. Also, the next generation follow-on to MidasPlus, called Chimera, is scheduled for release in 2000. It will run on some UNIX platforms as well as Windows NT.

Cn3D: This program, developed at the National Center for Biotechnology Information (NCBI), is a helper application for web browsers. It allows viewing of structures that are in ASN.1 format, such as those in NCBI's Molecular Modeling DataBase (MMDB). It is available for UNIX, Windows, and MacOS.