On Oct 1, 2009, at 7:51 PM, Charlie Bond wrote:
A note of caution: if a program doesn't show something as a beta strand that must mean that that part of the molecule doesn't have the attributes for strand. Rather than cosmetically fix it by changing it in pymol, it might be a good idea to look closely at the structure/density and see if the model can be improved.
This is good general advice, but in the specific case of pymol, the manual says:
'It is recommended that you read in PDB files which already have correct secondary structure assignments from a program like DSSP. However, PyMOL does have a reasonably fast secondary structure alignment algorithm called "dss". Please be aware that due to the subjective nature of secondary structure assignment in borderline cases, dss results will differ somewhat from DSSP.'
http://pymol.sourceforge.net/newman/user/S0260cartoons.html This may help: http://structure.usc.edu/dssp2pdb/ James
