Protein Secondary Structure Analysis

Cornelius Krasel krasel at alf.biochem.mpg.de
Wed Sep 14 13:02:17 EST 1994

micha at amber.biophys.uni-duesseldorf.de wrote:
: Michael West (micky at berthaw.princeton.edu) wrote:
: : Does anyone know of a program which will read a protein's pdb file, and then
: : make secondary structure assignments to each amino acid?  Any suggestions or
: : information would be appreciated.  Thanks.

: I fear that what I can point you to will be more than you are looking for,
: but try:

: There is a molecular graphics package called RasMol available on anonymous
: ftp space which is capable of 
: a) rendering the pdb file on a X display (unix) or on your windows screen,
: and 
: b) drawing ribbons, colouring the backbone, ribbon or whatever according to
: the residue's properties - among other properties, the secondary structure
: _is_ available.

I think the secondary structure assignments of Rasmol are taken from the PDB

The program you want to get is probably DSSP which is also available from
embl ftp server.

Sorry, I am not a crystallographer so I can't give more information :-/
People from the Sanders group are reading this and will probably soon correct
me ...


/* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */
/* email: krasel at alf.biochem.mpg.de                 fax: +49 89 8578 3795 */
/* "People are DNA's way of making more DNA." (Edward O. Wilson, 1975)    */

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