[chimerax-users] [Chimera-users] Color volume series by per voxel variance?

[Tom Goddard]

Hi Oli,

  Here is something similar I tried to see the motion in lightsheet microscopy of neutrophil-like cells crawling in collagen.

	https://www.cgl.ucsf.edu/chimera/data/mullins/cactus-oct2014/cactus.html <https://www.cgl.ucsf.edu/chimera/data/mullins/cactus-oct2014/cactus.html>


Done with the ChimeraX (or Chimera) measure motion command

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#motion <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#motion>

   Tom



> On Nov 23, 2021, at 8:40 AM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Thanks Elaine - maybe that will work... calculating a local correlation value between the first and last frame and then coloring all frames by volume data value. Will give it a go!
> 
> Cheers
> Oli
> 
>> On Nov 23, 2021, at 11:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Oli,
>> Not to my knowledge... The closest thing I can think of is ChimeraX "volume localCorrelation" (or in Chimera, "vop localCorrelation"), which compares two maps, and probably just opened as separate datasets rather than as part of a series:
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation>
>> 
>> ChimeraX has a "vseries measure" command but it gives centroids, surface areas, and enclosed volumes for the individual maps rather than any collective measures of variability.
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/vseries.html#measure>
>> 
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Nov 23, 2021, at 8:13 AM, Oliver Clarke via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hi all,
>>> 
>>> Is there any way in either Chimera or X to calculate the per voxel variance of a volume series, and then use that to color the individual voxels in each frame?
>>> 
>>> When one has a series of volumes showing a subtle conformational change - lets say identified using cryoDRGN or 3D variability analysis in cryoSPARC - it would be nice to be able to visually highlight on the map the region that is changing the most, in some kind of quantitatively sound way. 
>>> 
>>> Often local changes are visually apparent when looking at the maps and rotating them around, but don't necessarily stand out in a movie of the whole volume.
>>> 
>>> Coloring the series of maps (which are all on the same grid) by the variance of the density value at each voxel might be one way to visualize this. Is this possible?
>>> 
>>> Cheers
>>> Oli
>> 
> 
> 
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