On Jan 24, 2012, at 4:00 PM, Ed Pozharski wrote:
> I am looking for a program/server that would determine secondary
> structure from a pdb file and then output a new pdb file with
> HELIX/SHEET records. I have a model for which pymol fails to produce
> correct secondary structure. DSSP and STRIDE identify the secondary
> structure correctly but I'd need to convert their output myself to
> either pdb header or pymol script. So I wonder maybe something like
> that already exists.
If you open the PDB in Chimera and the PDB lacks HELIX/SHEET records,
Chimera will use DSSP to compute the secondary structure and if you
then save a new PDB file (File->Save PDB) the saved file will have the
appropriate HELIX/SHEET records. You can get Chimera from www.cgl.ucsf.edu/chimera
.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
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