VOLUME

Advisory 2006.10.12

You can download access and volume from our web page, following links at http://www.csb.yale.edu/download/download_descrip.html. The programs are unsuported, and have been compiled for SGI/IRIX 5.x. It should be possible to compile them for linux, perhaps with a little work.

It is likely that other, newer programs exist that would be more suitable. The Protein Data Bank has a list of useful software. See: http://www.rcsb.org/pdb/software-list.html#Analysis. Several possibilities include:
    http://monte.biochem.wisc.edu/~tsodikov/surface.html
    http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html
    http://www.ccl.net/cca/software/UNIX/pass/overview.shtml

The program VOLUME calculates the volume of a polyhedron surrounding each atom in a protein model. The algorithm is based on the procedure described by Voroni.

VOLUME was written by F.M. Richards as a companion to ACCESS and the output file of ACCESS serves as the input file for VOLUME.

The documentation for VOLUME is here.

To use VOLUME do the following:

Run ACCESS first to obtain the output file from that program.

Then simply type

    volume

and follow the prompts. Your input file will be the same as the output file from ACCESS. Read the documentation for a description of the options at each prompt.

An accessory program called VOLFMT will summarize the atom output of VOLUME to residue summaries of volumes.

After you have run VOLUME and have the output in a file, simply type:

     volfmt

and give the name of the VOLUME output file as the input file when prompted.

Please Note: If you publish results from this program please cite one of the following:

RICHARDS, F.M. J. Mol. Biol. 82: 1 - 14 (1974) The Interpretation of Protein Stuctures: Total Volume, Group Volume Distributions and Packing Density.

RICHARDS, F.M. Methods in Enzymology 115: 440-464 (1985) Calculation of Molecular Volumes and Areas for Structures of known Geometry.

Last Modified: Thursday, 12-Oct-2006 10:43:05 EDT

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