Hi Anindito, I still don't know what information is in your PDB (or mmCIF) file or in your map file, so it's still not possible to give you an exact command. Although you personally know that the map is C6, the map file probably doesn't have this annotation inside the file. If your map is #0 and atomic structure is #1 here are some possible commands to try but I really don't know if they will work. measure symmetry #0 Hopefully this would assign C6 symmetry to your map, if it can be recognized: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry> If the above worked, then maybe sym #1 group #0 If trying to put the symmetry on the map first doesn't work, then maybe sym #1 group C6 [**other options needed to give symmetry axis and symmetry center**] It can be difficult to figure out the axis and center and specify those in the command, which is why I suggested trying to detect it automatically for the map first. I don't know what the center and axis would be, it depends on your data. The format of specifying them is described in the "sym" help <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.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 Jan 21, 2022, at 12:01 PM, Sen, Anindito via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

HI Elaine,

I have docked the relevant atomic structure in the computed density map of C6 symmetry. I will now need to generate another 5 copies of the atomic structure to fit in the density envelope. And I was looking for the complete command. Let me know what will be the command.

Stay safe & Regards

Anindito Sen. Ph.D

Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257

Office: ILSB Room 1133 Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu

From: Elaine Meng <meng@cgl.ucsf.edu> Reply-To: "chimera-users@cgl.ucsf.edu List" <chimera-users@cgl.ucsf.edu> Date: Friday, January 21, 2022 at 12:30 PM To: "Sen, Anindito" <andysen@tamu.edu> Cc: "chimera-users@cgl.ucsf.edu List" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Making copies of an atomic structure and fit in the map

ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd Hi Anindito. We couldn't say what the "sym" command would be without knowing what information is in the structure file (PDB or mmCIF). If there is not symmetry information in the file then you have to specify it in the command instead, which can be difficult.

However, maybe what you really want is "fitmap" with symmetrical fitting (instead of making copies with "sym" first). In that case your density map must have symmetry information. See "fitmap" help and video: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/UsersGuid... > <https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimera/videodoc/SymFit... >

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

Begin forwarded message:

From: "Sen, Anindito" <andysen@tamu.edu> Subject: Making copies of an atomic structure and fit in the map Date: January 20, 2022 at 4:08:11 PM PST To: Chimera-users <chimera-users-bounces@cgl.ucsf.edu>

Dear All,

What will be the correct complete command (sym) for making copies of an atomic structure and symmetrize them to dock in the relevant density map.

Stay safe & Regards

Anindito Sen. Ph.D

Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257

Office: ILSB Room 1133 Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu

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