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. Elaine 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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