[chimerax-users] Manually imposed symmetry

[Shahid Khan]

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 <meng at cgl.ucsf.edu> 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 <smkhan at lbl.gov> 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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