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

[Oliver Clarke]

Nice this exactly what I was looking for, thank you Tom!!

Cheers
Oli

> On Nov 24, 2021, at 3:27 AM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Here is an example Python script to add a "volume variance" command to ChimeraX.
> 
> 	https://rbvi.github.io/chimerax-recipes/variance/variance.html
> 
>   Tom
> 
> 
> 
>> On Nov 23, 2021, at 3:08 PM, Oliver Clarke via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Thanks Tom for the cactus idea I will give that a go! Not sure where to start with computing the per pixel variance but will do some digging into the docs
>> 
>> Cheers
>> Oli
>> 
>>> On Nov 23, 2021, at 1:06 PM, Tom Goddard <goddard at sonic.net> wrote:
>>> 
>>> It would not be hard for ChimeraX to compute the per-pixel variance map with a little Python script.  Then you could use that to color your movie map surface by variance map value.
>>> 
>>> 	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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>>> 
>> 
>> 
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