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@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@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