Re: [Chimera-users] Coloring map by curvature
Hi Joel, I don't think surface curvature will be helpful understand the differences between two EM maps. But I was curious what it would look like. So here's a Python script and an image on a simulated map at 15 Angstroms. You use the script by opening your map, selecting the surface (ctrl-click on it), then open the curvature.py script (menu File / Open…). Here's a description of the method it uses from the comments at the top of the curvature.py file. # Color selected surface pieces by mean curvature. # # Gray at the average curvature value over the surface, and blue and red # at +/- 3 standard deviations of curvature values across the surface. # # The curvature is estimated from the vertices and normals of the triangulated # surface in simple way which will show artifacts from non-isotropic meshes. # For each triangle edge it computes the normal vector rotation from one vertex # to the other divided by the edge length. The vertex mean curvature is the # mean of the curvatures computed for each edge. # And the steps to make the example image open 1grl molmap #0 15 grid 2 model #1 select #1 open ~/Desktop/curvature.py Tom On Jan 29, 2014, at 9:40 AM, Joel Meyerson wrote:
Hi Darrell, 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. Joel
On Wed, Jan 29, 2014 at 11:44 AM, Hurt, Darrell (NIH/NIAID) [E] wrote: 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
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)" Date: Tuesday, January 28, 2014 9:08 PM To: Tom Goddard Cc: "chimera-users@cgl.ucsf.edu List" <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 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
Tom, This works beautifully! In the case of the two conformations I'm viewing, it provides very useful information. Thanks again. Joel On Wed, Jan 29, 2014 at 3:31 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Joel,
I don't think surface curvature will be helpful understand the differences between two EM maps. But I was curious what it would look like. So here's a Python script and an image on a simulated map at 15 Angstroms. You use the script by opening your map, selecting the surface (ctrl-click on it), then open the curvature.py script (menu File / Open...). Here's a description of the method it uses from the comments at the top of the curvature.py file.
# Color selected surface pieces by mean curvature. # # Gray at the average curvature value over the surface, and blue and red # at +/- 3 standard deviations of curvature values across the surface. # # The curvature is estimated from the vertices and normals of the triangulated # surface in simple way which will show artifacts from non-isotropic meshes. # For each triangle edge it computes the normal vector rotation from one vertex # to the other divided by the edge length. The vertex mean curvature is the # mean of the curvatures computed for each edge. #
And the steps to make the example image
open 1grl molmap #0 15 grid 2 model #1 select #1 open ~/Desktop/curvature.py
Tom
On Jan 29, 2014, at 9:40 AM, Joel Meyerson wrote:
Hi Darrell, 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. Joel
On Wed, Jan 29, 2014 at 11:44 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:
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
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)" Date: Tuesday, January 28, 2014 9:08 PM To: Tom Goddard Cc: "chimera-users@cgl.ucsf.edu List" <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 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
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Tom Goddard