I can only reiterate my first reply: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005149.html> Sorry I don't have anything more specific to tell you, Elaine On May 7, 2010, at 6:27 AM, Tom Duncan wrote:
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.