[Chimera-users] Making copies of an atomic structure and fit in the map

[Elaine Meng]

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://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#symmetric>
<https://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/>

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 at 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 at 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