README.clashlistcluster Home Page: Richardsons' Laboratory J. Michael Word - 6/1999


Clashlistcluster is a simple UNIX script which uses the awk facility along with the programs Probe and Cluster to build lists of van der Waals clashes from an input PDB-format molecular data file (with H atoms). These lists are organized such that collections of interacting residues are grouped together, sorted by the worst clash. For the purposes of this analysis, a clash is defined as a van der Waals overlap ≥ 0.4 Å.


The input file needs to have all H atoms; therefore, first run Reduce:

reduce -build xyz.pdb >xyzH.pdb

Then run clashlistcluster:

clashlistcluster xyzH.pdb name > xyzH.clcl

"Name" is an identifier which will be put at the start of each output line; however, that parameter may just be left out. The output file is plain ascii text for reading or printing. At the end is a summary of overall clash score (with and without omitting high-B atoms), number of atoms, etc.

Further information

Both source code and executable programs (for several operating systems) for Probe and Cluster can be found on the Richardson web and FTP sites. Get the latest version of the clashlistcluster script along with the programs Cluster, Probe and Reduce from:

J. Michael Word or
David C. Richardson
Biochemistry Department
Duke University
Durham, NC USA 27710