[Chimera-users] Coloring map by curvature

[Hurt, Darrell (NIH/NIAID) [E]]

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

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office: 301-402-0095
Mobile: 301-758-3559
Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
Twitter: @niaidbioit<https://twitter.com/niaidbioit>

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users