[Chimera-users] ksdssp assignments

Elaine Meng meng at cgl.ucsf.edu
Thu May 6 15:32:04 PDT 2010

At first I thought you meant you ran DSSP yourself.  How do you know  
that the secondary structure in the PDB file of 1aqt came from DSSP?   
I thought that PDB structure depositors were at liberty to define  
secondary structure as they wished, which could be done with several  
different programs or even based on subjective opinions.  In that  
case, it is not at all surprising for there to be differences, within  
reason.  I could be mistaken about the PDB protocol, however.

On May 6, 2010, at 3:22 PM, Elaine Meng wrote:

> 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
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