[chimera-dev] using chimera to display tomography map

[Tom Goddard]

Hi Wei,

  If you placed the copies of the subtomogram average, you could then use the Chimera "vop add" command to add them all together (or maybe better to use "vop maximum" so that the overlaps between two copies don't create double density) making a single map.  Then the "vop localCorrelation" command could compute the correlation between this assembled map and the original tomogram and color according to that correlation using the Chimera "Surface Color" tools to color by volume data value (using the local correlation map as the value).

  Chimera does almost nothing with Euler angles, and there are different Euler angle conventions you would need to worry about.  You would be better off if you had a 3x3 rotation matrix.  There is some Euler angle example of rotating a map and resampling it in the Chimera Python scripts web page but that seems like a hard approach.

	http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/eulermove.py

  Tom


> On Jan 2, 2020, at 10:08 AM, Wei Zhang <zhangwei at umn.edu> wrote:
> 
> Elanie,
> 
> These functions are very very useful. Thank you.
> I believe we can take advantage of these built-in functions in our procedures.
> 
> I have a follow-up question. If I have map (in mrc format), I wish to display it in Chimera at specific x, y, z position and at a certain Eular angle. How can I do it?
> I can think of two ways:
> (1) Modify the header of the map to include the position and orientation of the map, so Chimera can read and display it accordingly
> (2) Have a special text file that include those information and have Chimera display it 
> 
> Is there a better way to do it?
> 
> Thanks so much!
> 
> Wei
> 
> 
> On Thu, Jan 2, 2020 at 11:56 AM Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
> 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/UsersGuide/midas/vop.html#localCorrelation>>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html>>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.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/volume.html#localCorrelation>>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map <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 <mailto: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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