[chimera-dev] using chimera to display tomography map

[Wei Zhang]

Dear Elaine and Tom,

Thanks so much for the clarification and detailed information with the
links of the python scripts.
The algorithm becomes more refined. I will work though your emails step by
step. although there
is a learning curve.  I understand euler angle can be painful to work with
sometimes, thanks for
suggesting to convert them into a 3 by 3 rotation matrix. I will see how to
do it.

Best regards,

Wei


On Thu, Jan 2, 2020 at 3:14 PM Tom Goddard <goddard at sonic.net> wrote:

> 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> 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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