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

[Elaine Meng]

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 at 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 at cgl.ucsf.edu>
> Reply-To: "chimera-users at cgl.ucsf.edu List" <chimera-users at cgl.ucsf.edu>
> Date: Friday, January 21, 2022 at 12:30 PM
> To: "Sen, Anindito" <andysen at tamu.edu>
> Cc: "chimera-users at cgl.ucsf.edu List" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Making copies of an atomic structure and fit in the map
>  
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> 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/UsersGuide/midas/fitmap.html*symmetric__;Iw!!KwNVnqRv!UOhSQHX1qxC6PyIRYSi9YTK5pEIbS8YjJ4J4Hck_5Zqx8j0ahi9SHpEVmVEkrEQ$ >
> <https://urldefense.com/v3/__https://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/__;!!KwNVnqRv!UOhSQHX1qxC6PyIRYSi9YTK5pEIbS8YjJ4J4Hck_5Zqx8j0ahi9SHpEVZqAfnpQ$ >
>  
> 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
>  
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