[phenixbb] Secondary Structure Definitions

Nathaniel Echols nechols at lbl.gov
Thu May 3 09:00:46 PDT 2012

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
<Antony.Oliver at sussex.ac.uk> 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: antony.oliver at sussex.ac.uk
> tel (office): +44 (0)1273 678349
> tel (lab): +44 (0)1273 677512
> On 5/3/12 4:49 PM, "Nathaniel Echols" <nechols at lbl.gov> wrote:
>>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.
>>phenixbb mailing list
>>phenixbb at phenix-online.org
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