[chimerax-users] Manually imposed symmetry

[Shahid Khan]

 Good idea. Will do. Thanks, Tom.

Shahid

On Mon, Sep 16, 2019 at 6:57 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Shahid,
>
>   There is no ChimeraX tool to segment a map and take account of
> symmetry.  As Elaine mentioned you could try the ChimeraX Segment Map
> tool.  The author of that tool Greg Pintilie tried adding an option for it
> to use symmetry but decided it was not worth the trouble since even without
> that option it usually gives a mostly symmetric result when segmenting a
> symmetric map.
>
>   To see if the map symmetry is right I would suggest placing one copy of
> an atomic model in the map, then using the sym command to copy the placed
> atomic model using the map symmetry and see if the placements follow the
> map symmetry.  For example if #1 is the map and #2 is the atomic model.
>
> sym #2 symmetry #1
>
>   Tom
>
>
> On Sep 16, 2019, at 3:53 AM, Shahid Khan  wrote:
>
> Hello Elaine
>
> 1) Thanks for the correction of the syntax for setting the symmetry.
> Chimera-X does accept C33, but fitmap , with the "symmetric true" option,
> of the PDB structure that I want to model into the map gives a slightly
> wonky result. Maybe even though C33 is accepted the symmetry has been
> properly applied?
>
> 2) I do not want to use the Segment Map tool as the initial segmentation
> is automatic if I understand correctly. Is there a command or set of
> commands by which once I have manually assigned the C33 symmetry, I can
> segment of visualize the unit cell? This would give us the capability to
> utilize fitmap with greater confidence.
>
> Thanks
>
> Shahid
>
> On Wed, Sep 11, 2019 at 6:34 PM Elaine Meng  wrote:
>
>> Hi Shahid,
>> (1) The “symmetry” option of the “volume” command only marks the
>> specified map with the specified symmetry —  it does not split or segment
>> that map, so I don’t understand the series of actions you are trying to
>> perform.  The command also looks wrong.  Is the map #1?   (Does C33 =
>> 33-fold cyclic symmetry even exist??)
>>
>> If the map is #1 and you wanted C33 symmetry, command syntax would be
>> something like:
>>
>> volume #1 symmetry C33 axis z centerIndex 107.5
>>
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions>
>>
>> (2) it depends what mean by “created segments” … how did you create
>> them?  If you used the Segment Map tool, it has its own File menu with
>> options for saving:
>> <http://rbvi.ucsf.edu/chimerax/docs/user/tools/segment.html>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> > On Sep 11, 2019, at 5:24 AM, Shahid Khan wrote:
>> >
>> > Hello
>> >
>> > I am having difficulty in manually imposing symmetry on a map (*.mrc
>> file) and then extracting the unit cell for the subsequent fitting of PDB
>> structures with fitmap.
>> >
>> > (1) When I use the command
>> > "Volume symmetry #1, C33 axis z centerIndex 107.5"
>> >
>> > I get the error message "No placements for #1" that I do not understand.
>> >
>> > (2) I cannot figure out from the help documentation on how to save and
>> display one of the created segments.
>> >
>> > Any ideas? Thanks
>> >
>> > Shahid
>>
>>
>
> --
> Dr Shahid Khan
> Senior Scientist
> Molecular Biology Consortium
> Lawrence Berkeley National Laboratory
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>

-- 
Dr Shahid Khan
Senior Scientist
Molecular Biology Consortium
Lawrence Berkeley National Laboratory
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