PDBtool - Macromolecular Structure Browsing and Verification - v1.0

PDBtool is supported by the San Diego Supercomputer Center
Last Update July 23, 1996

What is PDBtool

PDBtool supports the browsing querying and verification (mainly geometry) of macromolecular structure data as found in files from the Protein Data Back (PDB). Key features are:

Browsing of structural components, namely, polypeptide chains (entities), individual residues (subentities), het groups and assigned secondary structure with corresponding highlighting in a 3-D viewer and renderer.
A variety of graphical and textual structure verification tools providing individual values, summaries and comparison to the standard values of Engh and Huber. In many cases values selected in the verification displays will be highlighted in the browsers and 3-D viewer. Displays are available for main chain and side chain geometries (lengths, angles , dihedrals), B values, disulphide linkages, and non-bonded contacts.
Limited querying by selection of specific amino acids or atom types.

Availability

Binaries: ftp://ftp.sdsc.edu/pub/sdsc/biology/PDBtool/
- Silicon Graphics Irix 5.x or later
- DEC Alpha UNIX
- SunOS 4.1 or later
Source: yes. Contact Phil Bourne

Note: Since this is an X/Motif application and X-terminal or other device supporting X can be used as a client. A color monitor is preferable.

More Information

J.Biggs, C.Pu, A Groeniger & P.E.Bourne J. App. Cryst. 1996, 29(4) 484-490. PDBtool: An Interactive Browser and Geometry Checker for Protein Structures.
Examples and Tutorial