PS. If you use this in publications, you should cite the original Kabsch and Sander DSSP paper - ksdssp is the same algorithm, as the name implies, and there isn't a separate publication (although I would mention the CGL in the acknowledgments). On Thu, May 3, 2012 at 8:52 AM, Antony Oliver wrote:

Dear Nat,

Excellent!  Thank you and the UCSF team.  I knew it would be in there somewhere!

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: [email protected] tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

On 5/3/12 4:49 PM, "Nathaniel Echols" wrote:

...

On Thu, May 3, 2012 at 8:35 AM, Antony Oliver wrote:

...

Is there a phenix jiffy to assign (and write!) secondary structure definitions to a pdb file?

phenix.ksdssp model.pdb

will output HELIX and SHEET records which you can paste into the PDB header.  You should verify the assignments yourself, however, as it occasionally runs adjacent helices together.

N.B.: Credit for this goes entirely to the UCSF computer graphics laboratory (http://www.cgl.ucsf.edu), developers of Chimera, but they were nice enough to release ksdssp under an unrestricted open-source license, so we distribute it with Phenix for use in generating secondary structure restraints.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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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: [email protected]mailto:[email protected] tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 From: Alexander Scouras mailto:[email protected]> Reply-To: PHENIX user mailing list mailto:[email protected]> Date: Thu, 3 May 2012 09:22:16 -0700 To: PHENIX user mailing list mailto:[email protected]> 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 mailto:[email protected]> 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: [email protected]mailto:[email protected] tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb