Re: [phenixbb] Secondary Structure Definitions

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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