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

[Sen, Anindito]

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
<http://microscopy.tamu.edu/>Tel. 979-458-9881
fax: 979-847-8933
http://microscopy.tamu.edu<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

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 ZjQcmQRYFpfptBannerStart
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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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