Cavities in proteins

[sgro at psl.wisc.edu]

In article <MAILQUEUE-101.930719101559.256 at legacy.calvin.edu>, grayt at legacy.Calvin.EDU ("Terry M. Gray") writes:
>Does anyone out there know how to determine cavity location and 
>cavity volumes in proteins?  I was told that the Conolly MS program 
>was needed and obtained a copy from QCPE.  
>
>I have not figured out how to determine internal cavity locations 
>and volumes with the output I get from MS.  In the manual there is 
>an obscure reference to "unit vectors normal to surface pointing 
>outward" that are required for volume measurement, but nothing 
>beyond that.  Is there a separate program for reading the "long" 
>output file so that cavity locations and volumes can be determined?
>
>I would like to be able to give a location of each cavity, i.e. the 
>coordinate of the center of the cavity and its size in cubic 
>Angstroms.  
>
>Thanks in advance for whatever help you can be.  
>
>
>Terry Gray  
>_____________________________________________________
>Terry M. Gray                                  
>Associate Professor of Chemistry
>Chemistry Department
>Calvin College
>3201 Burton Avenue SE
>Grand Rapids,  Michigan  49546
>Tel:  (616) 957-7187  FAX: (616) 957-8551

There is a much newer and bug-free package from Michael
Connolly that is "out". It is a package of different
programs bundled under the name "Molecular Surface
Package". A full description just appeared in:

Michael Connolly (1993) The Molecular Surface Package,
J. Mol. Graphics. Vol.11 (June 1993) pp 139-141.

The price is $850 for non profit, $1500 for non profit
abroad and $5000 for commercial users.
The address to ask for it is:

M. Connolly
2269 Chestnut street #279
San Francisco CA 94123 -USA-

The program pqms of the package calculates the cavities
as well as their volumes.
The program trb allows to triangulate the surface and
import the vectors into a visualization software package.

I hope this is useful

Jean-Yves Sgro

Institute for Molecular Virology
Madison Wi 53706 -USA-

608-262-7464 (voicez0
608-262-7414 (fax)

sgro at macc.wisc.edu

.