[Chimera-users] ksdssp assignments

Tom Duncan duncant at upstate.edu
Fri May 7 06:27:52 PDT 2010

On May 6, 2010, at 6:32 PM, Elaine Meng wrote:
> 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.

Sorry for the lack of details. I was referring the annotated sequence  
info for the PDB entry.
Example that I mentioned: http://www.pdb.org/pdb/explore/remediatedSequence.do?structureId=1AQT
It shows a DSSP cartoon of secondary structure above the sequence. I  
tried tweaking the parameters for ksdssp in Chimera (1.4) and could  
not get the same as shown with the PDB sequence.


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