[Q] secondary structure from coordinates
dalke at uxa.cso.uiuc.edu
Mon Nov 28 00:48:32 EST 1994
>In article <3ba23o$atq at vixen.cso.uiuc.edu>, dalke at uxa.cso.uiuc.edu (Andrew Dalke) writes:
>> I'm working on finding the secondary structure of an protein (helix,
>> sheet, etc.) given the atom coordinates.
To which Grant Jacobs <gjacobs at chmeds.ac.nz> replied
>I presume your problem is not working out the phi/psi angles, but what
>range of values ought to be a helix, etc.?
Absolutely correct. Finding the angles are easy; classifying them
> Maybe look up the ref. for
>PSSB (hope I've got the name right) - it ought to be by Chris Sander's
>group and see what they use.
I looked around on archie and some of the www searchers and couldn't
find a reference to PSSB. Could you point me out where to look?
> I'd be suprised if PDB don't supply a program to do this -
>the PDB or EMBL email/ftp servers...?
I looked in both of those FTP servers and couldn't find anything.
The closest was the "dihdrl" program at the pdb which will find the
What I would like is a list saying something like:
psi between X1 and Y1 & phi between A1 and B1 => helix
psi between X2 and Y2 & phi between A2 and B2 => helix
psi between X3 and Y3 & phi between A3 and B3 => beta sheet
dalke at ks.uiuc.edu
More information about the Proteins