<html><head></head><body bgcolor="#FFFFFF"><div>You can also directly tweak the assignments in pymol. "dss <object>" will run pymol's ad hoc structure assignment algorithm. It seems to be run automatically if you load files without ss headers, so is probably what you are already seeing. </div><div><br></div><div>Then you can fix it with "alter resi 5-10, ss='h'" &"rebuild". Especially useful if you disagree with the DSSP assignments. I dont know if pymol writes ss in the PDB headers yet when you save it though.</div><div><br></div><div><a href="http://www.pymolwiki.org/index.php/Dss">http://www.pymolwiki.org/index.php/Dss</a><br><div><br></div></div><div>Alexander D. Scouras</div><div>Postdoctoral Fellow</div><div>Alber Lab</div><div>University of California, Berkeley</div><div><br></div><div><br></div><div><br>On May 3, 2012, at 8:35 AM, Antony Oliver <<a href="mailto:Antony.Oliver@sussex.ac.uk">Antony.Oliver@sussex.ac.uk</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div>
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<div>Dear all,</div>
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<div>Is there a phenix jiffy to assign (and write!) secondary structure definitions to a pdb file?</div>
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<div>I'm currently using MacPyMOL to put together some figures, and I can see that some of the secondary structure elements in the cartoon representation aren't being drawn correctly.</div>
<div>Being slightly old-school, I used to use DSSP and the little program dssp2pdb to extract the information and put it into the PDB header.</div>
<div>Is there a simpler / easier way to do this? (NB: I'm aware that CCP4MG copes better with SS assignment, but I prefer to use PyMOL in this instance).</div>
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<div>With thanks, </div>
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<div>Tony.</div>
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Dr Antony W Oliver</div>
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