[chimerax-users] Manually imposed symmetry

[Elaine Meng]

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