[Chimera-users] Coloring map by curvature

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Wed Jan 29 08:44:17 PST 2014


Hi Joel,

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:
http://meshlabstuff.blogspot.com/2010/03/mean-curvature-cavity-map-zbrush-and.html

FWIW,
Darrell

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From: <Meyerson>, "Joel [F] (NIH/NCI)" <meyersonj at mail.nih.gov<mailto:meyersonj at mail.nih.gov>>
Date: Tuesday, January 28, 2014 9:08 PM
To: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> List" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] Coloring map by curvature

Hi Tom,
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.
Thanks!
Joel


On Tue, Jan 28, 2014 at 7:36 PM, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:
Hi Joel,

  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?

        Tom


On Jan 28, 2014, at 2:29 PM, Joel Meyerson wrote:

> Hi,
> Is it possible to color a map based on surface curvature?
> Thanks,
> Joel
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