Re: [Chimera-users] Breaking down symmetry in Chimera
Hi Anne, It is recommended to send Chimera questions to chimera-users@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 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#symmetric> and video tutorial <http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/> 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@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
Hi Anne, I think carving out 1/6 of the D3 symmetry map won’t help you because how will you know the boundaries to divide the map on? If you arbitrarily take a 1/6 of map asym unit you will almost surely have part two different monomers in it, and this 1/6 map won’t cover a single monomer, so you won’t be able to fit the monomer well since some of the density is missing. So as Elaine suggested, you want to work with the full map. A few other ideas to try are the fitmap command search option which places the atomic structure at random in the map and then locally optimizes it. Or you could try Segger within Chimera which will try to segment the map, maybe into 6 pieces that really do correspond to the monomers and then you can fit into one of the segments using Segger (menu Tools / Volume Data / Segment Map and Tools / Volume Data / Fit to Segments). Tom
On Dec 6, 2018, at 11:19 AM, Elaine Meng wrote:
Hi Anne, It is recommended to send Chimera questions to chimera-users@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 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html#symmetric>
and video tutorial <http://www.cgl.ucsf.edu/chimera/videodoc/SymFitDNAb/>
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 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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Thanks, The suggestions below were very helpful. Anne ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Thursday, December 6, 2018 1:53:26 PM To: chimera-users Cc: Jecrois, Anne Subject: Re: [Chimera-users] Breaking down symmetry in Chimera Hi Anne, I think carving out 1/6 of the D3 symmetry map won’t help you because how will you know the boundaries to divide the map on? If you arbitrarily take a 1/6 of map asym unit you will almost surely have part two different monomers in it, and this 1/6 map won’t cover a single monomer, so you won’t be able to fit the monomer well since some of the density is missing. So as Elaine suggested, you want to work with the full map. A few other ideas to try are the fitmap command search option which places the atomic structure at random in the map and then locally optimizes it. Or you could try Segger within Chimera which will try to segment the map, maybe into 6 pieces that really do correspond to the monomers and then you can fit into one of the segments using Segger (menu Tools / Volume Data / Segment Map and Tools / Volume Data / Fit to Segments). Tom
On Dec 6, 2018, at 11:19 AM, Elaine Meng wrote:
Hi Anne, It is recommended to send Chimera questions to chimera-users@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=dEoVfoDuDZ8vwe7BNzjWGR9jWgtdqcc9nWTGtB__geM&s=KO5Gepj2nshD3IMDTbBONlivH-umfB_Ytp4nMQpQyTo&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=dEoVfoDuDZ8vwe7BNzjWGR9jWgtdqcc9nWTGtB__geM&s=N2rj-998heWcjLH6jnmVuzXxcUWwi6ybePh354vL2oE&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 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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailm...
Thank you. The video was very helpful. Anne ________________________________ From: Elaine Meng <meng@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@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@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
participants (3)
-
Elaine Meng -
Jecrois, Anne -
Tom Goddard