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
