[chimera-dev] using chimera to display tomography map

[Tom Goddard]

Hi Wei,

  It looks to me that figure 1B of the HIV TRIM5alpha paper (attached below) has about 1000 copies of the subtomogram averaged hexamer placed to make the filament.  You can see in figure 1F, 1G, 1H a magnified version where the seams between the different hexamers are visible.

  There are some Python scripts for Chimera to place copies of a map at specific positions given by a rotation matrix and translation.  These scripts are on the Chimera Python scripts web page

	http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>

one is called "place.py" and another that works with IMOD placements is called "placeimod.py"

	http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/place.py
	http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/placeimod.py <http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/placeimod.py>

There are also scripts to place molecular models at each position.  I just searched for "copies" on that Chimera scripts web page to find these.

  For coloring the copies by their correlation with the tomogram you could use the Chimera "measure correlation" command once for each placed copy

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#correlation

You could make use of the perframe command to measure these all in one command or you could make a command file or Python script that ran all those commands. Then how do you color using correlation?  There is a Chimera Render by Attribute too and rangecolor command that can color molecules by an attribute value but those don't work on maps.  So I guess my best suggestion  for that would be to use a Python script that loops over the placed copies, computes their correlation, then colors them. I can help with that script if you want to try it.

  Another thought is to ask the authors of the HIV TRIM5alpha paper how they did it.

	Tom




> 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 <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
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