Wanted: program to extract secondary struct from pdb files

Peter Stockwell peter at sanger.otago.ac.nz
Sun May 22 15:28:25 EST 1994


matte at skyfox.usask.ca wrote:
> > Description: Wanted: program to extract secondary struct from pdb files

> > I am looking for a program that will take the atomic coordinates of PDB
> > files and calculate the secondary structure, based on phi and psi angles
> > of the residues. I have several PDB files that are missing the secondary
> > structure information, and I need this info for several of my programs. My
> > mentor told me that there was one such program developed by Kabsch and
> > Sander (EMBL, Heidelberg). Where can I find it, or any other program?

The Kabsch and Sander program DSSP is available:  I located it last week
using GOPHER to reach the EMBL Heidelberg server, and located the 
software/unix directory.  A dssp directory contains a license agreement and
a README file.  Retrieving these, printing and signing the license agreement
and FAXing it to the address given resulted in EMAIL distribution of the
dssp sources the following night.  The program has compiled and appears to 
work fine on the example file given.

Peter A. Stockwell

> > Thanks in advance.

> > Steven Adams, Graduate Student, Biochemistry, Baylor College of Medicine
> > email: sa690538 at bcm.tmc.edu


> 	There is a program developed at the Centre for Structural Biology,
> Yale University, called DEFINE_Structure which will do secondary structures
> based on c-alpha coordinates. See F.M. Richards and C.E. Kundrot Proteins
> 3:71-84 (1988) Identification of Structural Motifs from Protein Coordinate Data:
> Secondary Structure and First-Level  Supersecondary Structure. You will need
> to contact the authors and get permission to download the program from Yale;
> I believe there is no cost. 

> Hope this helps !

> -------------------------------------------------------------------------------
> | Allan Matte                          |                                      |
> | Department of Biochemistry           | Phone: (306)966-4366                 |
> | University of Saskatchewan           | Fax: (306)966-8718                   |
> | Saskatoon, Saskatchewan              | E-mail: matte at sask.usask.ca          |
> | CANADA S7N 0W0                       |                                      |
> -------------------------------------------------------------------------------




More information about the Xtal-log mailing list