[chimera-dev] using chimera to display tomography map

[Elaine Meng]

Hi Wei,
Happy 2020!

Chimera has a “vop localCorrelation” command that given two maps, creates a new map that is the local correlation (using a sliding box, for which the user can specify the box size).  Then the local-correlation map values can be used to color the isosurface of another map using the “Surface Color” tool or “scolor” command, and also show a color key.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#localCorrelation>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html>

ChimeraX also has these features, as commands “volume localCorrelation” and “color sample”, but cannot yet draw the color key.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#localCorrelation>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map>

I hope this helps,
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 1, 2020, at 8:40 AM, Wei Zhang <zhangwei at umn.edu> wrote:
> 
> Hello,
> Happy 2020!
> 
> We are doing tomography reconstruction of retrovirus assemblies. Because the raw tomograms are very noisy, they can not be represented nicely using isosurfaces. I see other researchers in the field presented the tomo map in Chimera by superimposing subtomogram-averaged map onto the original tomogram according to the subunit's locations and  relative orientations. The color of the displayed subunits is based on the correlation coefficient between the averaged subunit map and the original density of the tomogram.
> 
> One example is Fig.1B in this paper:
> https://advances.sciencemag.org/content/5/11/eaaw3631
> 
> We do use the program Dynamo for the subtomogram averaging procedure, so our data format is very similar to what was used in this paper. Is this feature is part of Chimera? Could we obtain the extended software? Or is this customer built and we need to contact the authors of the paper? Or shall we work out this procedure by ourselves with the help of Chimera experts?
> 
> Thank you,
> Wei