Re: [phenixbb] Secondary Structure Definitions

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