Cavities in proteins

[Terry M. Gray]

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