<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div></div><div><br><div><div>On Jan 29, 2014, at 9:40 AM, Joel Meyerson wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div>Hi Darrell,<br>Thanks for the tip! I hadn't considered mesh lab but that link you sent looks promising. I'll also wait to see if Tom has any further suggestions.<br></div>Joel<br></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Wed, Jan 29, 2014 at 11:44 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:<br>
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<div>Hi Joel,</div>
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<div>I love Chimera and use it all the time. However, a quick-and-dirty solution to your problem might be to try Meshlab. It is kind of buggy software, but can be very useful. Here's a tutorial/blog entry that I found in a quick search. At the very least, it
describes what I think Tom was communicating about enhancing surface shading:</div>
<div><a href="http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-and.html" target="_blank">http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-and.html</a></div>
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<div>FWIW,</div>
<div>Darrell</div>
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<div><span style="font-size:12px">-- </span></div>
<font><font style="font-size:12px" face="Calibri,Verdana,Helvetica,Arial">Darrell Hurt, Ph.D.<br>
Section Head, Computational Biology<br>
Bioinformatics and Computational Biosciences Branch (BCBB)<br>
OCICB/OSMO/OD/NIAID/NIH<br>
<br>
31 Center Drive, Room 3B62B, MSC 2135<br>
Bethesda, MD 20892-2135<br></font></font><div><font style="font-size:12px" face="Calibri,Verdana,Helvetica,Arial"><br>
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<span style="font-weight:bold">From: </span><Meyerson>, "Joel [F] (NIH/NCI)" <br>
<span style="font-weight:bold">Date: </span>Tuesday, January 28, 2014 9:08 PM<br>
<span style="font-weight:bold">To: </span>Tom Goddard <br>
<span style="font-weight:bold">Cc: </span>"<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a> List" <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>><div class="im">
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<span style="font-weight:bold">Subject: </span>Re: [Chimera-users] Coloring map by curvature<br>
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<div>Hi Tom,<br>
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I have cryo-EM maps for two conformations of a protein, both in the 15 Angstrom resolution range. The conformations are visibly different, but I am also interested in seeing where they differ in terms of their surface curvature, as it could have bearing on
how I interpret the conformations. If there's any other info I can provide just let me know.<br>
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Thanks!<br>
Joel<br>
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<div class="gmail_quote">On Tue, Jan 28, 2014 at 7:36 PM, Tom Goddard wrote:<br>
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Hi Joel,<br>
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No, Chimera does not compute surface curvature. It would not be too hard to make a Python script that computed it and used it to color a surface. The main trouble is defining numerically the curvature for a triangulated surface at each vertex. Why are
you interested in this? Is the idea to simulate ambient occlusion lighting where surface cavities are dark and projections are brighter? Is the idea to try it on EM maps or molecular surfaces?<br>
<br>
Tom<br>
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On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote:<br>
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> Hi,<br>
> Is it possible to color a map based on surface curvature?<br>
> Thanks,<br>
> Joel<br>
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