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