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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
file.

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.

--
/* 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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