[phenixbb] Secondary Structure Definitions

[Antony Oliver]

Thanks Alexander – I'm aware of the auto-assignment done by PyMOL.  IMHO, it does get this wrong quite a bit of the time, and I don't want to spend a lot of time re-assigning secondary structure assignments.
The phenix.ksdssp module seems a far simpler solution!

With many 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<mailto:antony.oliver at sussex.ac.uk>
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512


From: Alexander Scouras <scouras at berkeley.edu<mailto:scouras at berkeley.edu>>
Reply-To: PHENIX user mailing list <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Date: Thu, 3 May 2012 09:22:16 -0700
To: PHENIX user mailing list <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Subject: Re: [phenixbb] Secondary Structure Definitions

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.

http://www.pymolwiki.org/index.php/Dss

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<mailto: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<mailto:antony.oliver at sussex.ac.uk>
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512

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