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<div>Thanks Alexander – I'm aware of the auto-assignment done by PyMOL. IMHO, it does get this wrong quite a bit of the time, and I don't want to spend a lot of time re-assigning secondary structure assignments.</div>
<div>The phenix.ksdssp module seems a far simpler solution!</div>
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<div>With many thanks,</div>
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Dr Antony W Oliver</div>
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<span style="font-weight:bold">From: </span>Alexander Scouras <<a href="mailto:scouras@berkeley.edu">scouras@berkeley.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
<span style="font-weight:bold">Date: </span>Thu, 3 May 2012 09:22:16 -0700<br>
<span style="font-weight:bold">To: </span>PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [phenixbb] Secondary Structure Definitions<br>
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<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>
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<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>
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<div><a href="http://www.pymolwiki.org/index.php/Dss">http://www.pymolwiki.org/index.php/Dss</a><br>
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<div>Alexander D. Scouras</div>
<div>Postdoctoral Fellow</div>
<div>Alber Lab</div>
<div>University of California, Berkeley</div>
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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>
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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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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-family: Helvetica; font-size: medium; ">
Senior Research Fellow</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-family: Helvetica; font-size: medium; ">
CR-UK DNA Repair Enzymes Group</div>
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Genome Damage and Stability Centre</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-family: Helvetica; font-size: medium; ">
Science Park Road</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-family: Helvetica; font-size: medium; ">
University of Sussex</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; font-family: Helvetica; font-size: medium; ">
Falmer, Brighton, BN1 9RQ</div>
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email: <a href="mailto:antony.oliver@sussex.ac.uk">antony.oliver@sussex.ac.uk</a></div>
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