secondary structure output

From: Ed Pozharski
Date: 24 January 2012 20:57


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.

Gracias,

Ed




--
"I'd jump in myself, if I weren't so good at whistling."
                              Julian, King of Lemurs

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From: James Stroud


Try DSSP2PDB.

http://structure.usc.edu/dssp2pdb/


It's a perl script.

Crossover flame note: I spent a lot of time learning perl and I still don't recommend the language ;-)

James

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From: Martin Hällberg

You can try STRIDE2PyMOL:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/stride_ss.py

/Martin

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From: James Stroud 

This reminds me of stride2pdb in case you want to use more than pymol with your secondary structure assignments:

http://structure.usc.edu/stride2pdb/

James

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From: Eric Pettersen


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