Coloring map by curvature
Hi, Is it possible to color a map based on surface curvature? Thanks, Joel
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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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-an... 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.a...> 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@mail.nih.gov<mailto:meyersonj@mail.nih.gov>> Date: Tuesday, January 28, 2014 9:08 PM To: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> List" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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@sonic.net<mailto:goddard@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@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hey folks!!! You have got my email address mixed up with others...this is the second mysterious incomprehensible message meant for somebody else sent by a different advisor...fix it.....this one by Tom the other by a woman (I deleted the message - it was long one.........) Stay well......regards, Dennis -----Original Message----- From: chimera-users-bounces@cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Tom Goddard Sent: Tuesday, January 28, 2014 7:37 PM To: Joel Meyerson Cc: chimera-users@cgl.ucsf.edu List Subject: Re: [Chimera-users] Coloring map by curvature 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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
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Hurt, Darrell (NIH/NIAID) [E] -
Joel Meyerson -
Pollack, J -
Tom Goddard