[Chimera-users] ksdssp assignments

[Elaine Meng]

Hi Tom,
I don't know for certain, but a likely reason would be different  
parameters (cutoff energy, minimum helix length, minimum strand  
length).  Chimera does not use DSSP itself, but an implementation of  
what was described in the Kabsch & Sander paper.  I looked for DSSP  
documentation online and was unable to find anything about the  
parameter values it uses... does the DSSP output say anything about  
that, or can you guess from the differences you see?
Best
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 6, 2010, at 12:26 PM, Tom Duncan wrote:

> I noticed that the secondary structure assignments for a specific  
> protein by ksdssp (default parameters) show a few significant  
> differences versus the DSSP assignments shown at the PDB (file =  
> 1aqt). Any idea why?
> Thanks,
> Tom