[Chimera-users] Breaking down symmetry in Chimera

[Jecrois, Anne]

Thank you. The video was very helpful.

Anne

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, December 6, 2018 1:19:52 PM
To: Jecrois, Anne
Cc: chimera-users
Subject: Re: Breaking down symmetry in Chimera

Hi Anne,
It is recommended to send Chimera questions to chimera-users at cgl.ucsf.edu (CC’d here) since others may be able to provide better answers or benefit from the exchange.

My guess is that you might instead want to use symmetrical fitting, in which multiple copies of the atomic structure automatically maintain the specified symmetry.  Symmetrical fitting is available in the “fitmap” command (not the GUI).

See documentation
<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_fitmap.html&d=DwIFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=xj60DB44yQ0WTGDKKTw7d6XIxINCx14zZ9gq0mjPWKE&m=h6Zq_A4om9uurkWspgi6SpN97Yfyw53Ci31-94fHZ8E&s=RN2j_UDnLb7eayJpVQsnSpqnmMLgyEZjUESBFYrLQ_s&e=>
<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_fitmap.html-23symmetric&d=DwIFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=xj60DB44yQ0WTGDKKTw7d6XIxINCx14zZ9gq0mjPWKE&m=h6Zq_A4om9uurkWspgi6SpN97Yfyw53Ci31-94fHZ8E&s=sOmKLAKKNoKJLYEHKr6K1SbqErz6Eikh9lz7nsgE-rI&e=>

and video tutorial
<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cgl.ucsf.edu_chimera_videodoc_SymFitDNAb_&d=DwIFaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=xj60DB44yQ0WTGDKKTw7d6XIxINCx14zZ9gq0mjPWKE&m=h6Zq_A4om9uurkWspgi6SpN97Yfyw53Ci31-94fHZ8E&s=l3d5KE5dctu1Yw2T6wuFtg7Waf9JI8H89JKNC1uD7Ow&e=>

The video is >6 minutes but worth watching, because like in that video you may need to first just fit one copy (not using symmetry), then use command “measure symmetry” to annotate the map with its symmetry, and then use command “sym” with “update true” to generate the symmetry copies of the atomic model.

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

> On Dec 6, 2018, at 10:32 AM, Jecrois, Anne <Anne.Jecrois at umassmed.edu> wrote:
>
> Dear Dr Meng,
> I have a 5A cryoEM map with D3 symmetry, howeve I am having some problem with rigid body fitting since I don't know where one assymmetric unit starts or ends . I was wondering if there is way to break down the symmetry in chimera and extract 1/6 of the map and use that for fitting?
> Thanks,
> Anne Jecrois
> PhD Candidate
> UMass Medical School
> Schiffer Lab/Royer Lab
> 364 Plantation St, LRB 970L
> Worcester MA 01605

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