[phenixbb] Secondary Structure Definitions

Antony Oliver Antony.Oliver at sussex.ac.uk
Thu May 3 08:52:51 PDT 2012

Dear Nat,

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


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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