[phenixbb] Secondary Structure Definitions

Nathaniel Echols nechols at lbl.gov
Thu May 3 08:49:28 PDT 2012

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


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