[Chimera-users] ksdssp assignments
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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