[chimera-dev] using chimera to display tomography map

[Wei Zhang]

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> 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/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
>
>
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