[Chimera-users] Coloring map by curvature

Tom Goddard goddard at sonic.net
Wed Jan 29 12:31:32 PST 2014


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-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
> 
> 
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> 
> From: <Meyerson>, "Joel [F] (NIH/NCI)" 
> Date: Tuesday, January 28, 2014 9:08 PM
> To: Tom Goddard 
> Cc: "chimera-users at cgl.ucsf.edu List" <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 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
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> 

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