[Chimera-users] Coloring map by curvature

Joel Meyerson meyersonj at mail.nih.gov
Wed Jan 29 13:38:06 PST 2014


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