Important Note: QPACK may be available via anonymous ftp and it is free to academic users. However, we would like all sites to be licensed. If you have obtained QPACK via anonymous ftp and have not contacted us to receive a license agreement, please do so at Academic Software Licensing. If this fails to do what you want, or you would like to discuss a commercial license, please contact us about other licensing agreement.
There are two versions: a unix version and a VMS version. The distribution
contains the three programs described in "A Novel Method for the Rapid Evaluation
of Packing in Protein Structures" by Lydia M. Gregoret and Fred E. Cohen J.
Mol. Biol. 211:959-974, 1990.
The directory "cofm" contains the program "cofm" which stands for "center of mass." Cofm reads a PDB file and writes the coordinates of the centroids of the residues (again in PDB format).
The directory "qpack" contains the program "qpack" (Quick Pack) which
performs a packing evaluation on a structure. Qpack takes the output
from cofm as input. It can generate output in three different formats:
PDB format, a "short" format containing vital information, and a list
of contact pairs.
The directory "libpdb" contains the UCSF Computer Graphics Lab routines for reading and writing pdb files. Qpack and cofm must be linked with the routines in this directory. Also, the definition file "pdb.h" required by qpack and cofm is in this directory. The file "pdb.3" is a short Unix man page about this library of functions.
The directory "sumpairs" contains the program "sumpairs" which reads a
list of residue contact pairs (output from qpack) and a pair potential
matrix file. It computes the "pair potential sum" for a structure.
The directory "midas" contains two scripts that enable a user of UCSF MidasPlus to execute qpack from within MidasPlus and color a molecule according to packing density.
All of these directories contain additional help information.
Lydia Gregoret
Oct. 23, 1989
Qpack updated to version 1.1
Monday July 16 12:54:14 PM 1990