structure calculation

Andrew Martin martin at bsm.bioc.ucl.ac.uk
Mon May 22 11:17:09 EST 1995

chan at bioch.ox.ac.uk wrote:
: Hi there,

: Can anyone tell me is there a software that can calculate the phi and psi 
: angles of each amino acid residue from pdb files. The reason is that I 
: want to know which strach of amino acid is alpha-coil, beta-sheet, turn 
: and random coil _calculated_ from the pdb files. That means, not 
: prediction. I have try to extract the molscript file from rasmol, but the 
: result is not very good.

: Thanks in advance!

There have been a number of responses to this post! If what you want
is the secondary structure assignments, then you probably do want
DSSP as suggested in one of the followups, but this basically works
on H-bonding patterns and not on phi/psi angles.

If you do want to know torsion angles, then there is a rather crude
FORTRAN program distributed with the PDB (or there certainly used to
be!). Alternatively, you could indeed use your own program written
in Modula2 as Dave Webster suggested (though I think he must be
about the only person in protein structure to use Modula2 - sorry
Dave), or C, or whatever. I have a program which will do the job in
C and would be happy to send you a copy.

Another simmple DSSP-based way is to use the Rasmol program which
uses the DSSP algorithm and will colour your structure on SS-type.

Why not speak to people in Biophysics in Oxford; they're sure to
have something.

Best wishes,


: **********************************************************************
: *         2	*	Christopher Chan			     *
: *   CCCCC	*	Dept. of Biochemistry			     *
: *   C		*	University of Oxford			     *
: *   C		*	Oxford					     *
: *   C		*	U.K.					     *
: *   CCCCC	*	Tel.: 0865-(2)75239			     *
: *		*	E-mail: chan at bioch.ox.ac.uk		     *
: **********************************************************************
: ----- PGP public key available upon request -----

Dr. Andrew C.R. Martin,         University College London & SciTech Software
EMAIL: martin at biochem.ucl.ac.uk          Tel: (Work) +44(0)71 387 7050 X3284
URL: http://www.biochem.ucl.ac.uk/~martin     (Home) +44(0)372 275775

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