Wanted: program to extract secondary struct from pdb files

[norm eberhardt]

In article <17MAY94.19471341 at skyfox.usask.ca>, matte at skyfox.usask.ca writes:
|> > 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?
|> 
|> > 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                       |                                      |
|> -------------------------------------------------------------------------------

	Try DSSP available from EMBL.  You can get the license via anonymous 
ftp from ftp.embl-heidelberg.de in pub/software/unix/dssp.  Follow the
instructions and the software will be forwarded by e-mail.  If you want further
information on the program, see Kabsch and Sander, Biopolymers 22:2577-2637
(1983).  The program has been updated and works very well to accomplish your aims.

norman eberhardt
eberhardt at mayo.edu