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

Good idea. Will do. Thanks, Tom.

Shahid

On Mon, Sep 16, 2019 at 6:57 PM Tom Goddard goddard@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users