[phenixbb] Secondary Structure Definitions

Alexander Scouras scouras at berkeley.edu
Thu May 3 09:22:16 PDT 2012

You can also directly tweak the assignments in pymol. "dss <object>" will run pymol's ad hoc structure assignment algorithm. It seems to be run automatically if you load files without ss headers, so is probably what you are already seeing. 

Then you can fix it with "alter resi 5-10, ss='h'" &"rebuild". Especially useful if you disagree with the DSSP assignments. I dont know if pymol writes ss in the PDB headers yet when you save it though.


Alexander D. Scouras
Postdoctoral Fellow
Alber Lab
University of California, Berkeley

On May 3, 2012, at 8:35 AM, Antony Oliver <Antony.Oliver at sussex.ac.uk> wrote:

> Dear all,
> Is there a phenix jiffy to assign (and write!) secondary structure definitions to a pdb file?
> I'm currently using MacPyMOL to put together some figures, and I can see that some of the secondary structure elements in the cartoon representation aren't being drawn correctly.
> Being slightly old-school, I used to use DSSP and the little program dssp2pdb to extract the information and put it into the PDB header.
> Is there a simpler / easier way to do this?  (NB: I'm aware that CCP4MG copes better with SS assignment, but I prefer to use PyMOL in this instance).
> With thanks, 
> Tony.
> ---
> Dr Antony W Oliver
> Senior Research Fellow
> CR-UK DNA Repair Enzymes Group
> Genome Damage and Stability Centre
> Science Park Road
> University of Sussex
> Falmer, Brighton, BN1 9RQ
> email: antony.oliver at sussex.ac.uk
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