symmetrizing the model
Dear colleagues,
A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application?
I found the one for Chimera but not for ChimeraX.
Many thanks.
Sincerely, Dmitry
Hi Dmitry, If you mean to create symmetry copies of an atomic model, it's basically the same command in ChimeraX as in Chimera, "sym", but with some small differences in the options and how you would specify them.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html
The easiest case is if the symmetry is already defined in the mmcif structure, e.g.:
open 1fav sym #1 assembly 1
... which by default will create a new model 2 that contains the assembly. There are lots of options, however, including whether it should be a new model or not, so you should look at the help page.
If the symmetry is not defined in the mmcif atomic structure file, you can specify symmetry group and parameters directly in the command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry
Example:
sym #1 C5 center 0,0,0
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2023, at 2:06 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues, A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application? I found the one for Chimera but not for ChimeraX. Many thanks. Sincerely, Dmitry
Dear Elaine,
Many thanks for this explanation and examples.
Does ChimeraX also have the option to symmetrize the cryo-EM 3D maps? If yes - what commands are used for this purpose?
Kind regards, Dmitry
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: 22 September 2023 16:49 To: Dmitry Semchonok semchonok@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] symmetrizing the model
Hi Dmitry, If you mean to create symmetry copies of an atomic model, it's basically the same command in ChimeraX as in Chimera, "sym", but with some small differences in the options and how you would specify them.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html
The easiest case is if the symmetry is already defined in the mmcif structure, e.g.:
open 1fav sym #1 assembly 1
... which by default will create a new model 2 that contains the assembly. There are lots of options, however, including whether it should be a new model or not, so you should look at the help page.
If the symmetry is not defined in the mmcif atomic structure file, you can specify symmetry group and parameters directly in the command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry
Example:
sym #1 C5 center 0,0,0
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2023, at 2:06 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues, A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application? I found the one for Chimera but not for ChimeraX. Many thanks. Sincerely, Dmitry
Hi Dmitry, As far as I know there is no option to symmetrize maps. I was only trying to clarify that my previous explanation was for atomic structures only. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2023, at 9:55 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Elaine,
Many thanks for this explanation and examples.
Does ChimeraX also have the option to symmetrize the cryo-EM 3D maps? If yes - what commands are used for this purpose?
Kind regards, Dmitry
From: Elaine Meng meng@cgl.ucsf.edu Sent: 22 September 2023 16:49 To: Dmitry Semchonok semchonok@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] symmetrizing the model
Hi Dmitry, If you mean to create symmetry copies of an atomic model, it's basically the same command in ChimeraX as in Chimera, "sym", but with some small differences in the options and how you would specify them.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html
The easiest case is if the symmetry is already defined in the mmcif structure, e.g.:
open 1fav sym #1 assembly 1
... which by default will create a new model 2 that contains the assembly. There are lots of options, however, including whether it should be a new model or not, so you should look at the help page.
If the symmetry is not defined in the mmcif atomic structure file, you can specify symmetry group and parameters directly in the command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry
Example:
sym #1 C5 center 0,0,0
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2023, at 2:06 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues, A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application? I found the one for Chimera but not for ChimeraX. Many thanks. Sincerely, Dmitry
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Dmitry,
Elaine is right that there is no ChimeraX command specifically to symmetrize a map. But you probably can do it in a few ways in ChimeraX. For instance if you have a dimer map and want to symmetrize, open two copies and position the second one in the symmetry related orientation (e.g. rotate y 180 model #2) and add them with the ChimeraX "volume add" command (e.g volume add #1,2). Another approach for more complicated symmetries would be to assign the map symmetry with the "measure symmetry" or "volume symmetry" command, and then use the "volume cover" command to produce a new map which applies all the symmetries averaging the values, for example,
open 1080 from emdb measure symmetry #1 > Symmetry emdb 1080: D7, center 50 50 50 volume cover #1 ibox 0,0,0,99,99,99
Tom
On Sep 22, 2023, at 11:22 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dmitry, As far as I know there is no option to symmetrize maps. I was only trying to clarify that my previous explanation was for atomic structures only. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2023, at 9:55 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Elaine,
Many thanks for this explanation and examples.
Does ChimeraX also have the option to symmetrize the cryo-EM 3D maps? If yes - what commands are used for this purpose?
Kind regards, Dmitry
From: Elaine Meng meng@cgl.ucsf.edu Sent: 22 September 2023 16:49 To: Dmitry Semchonok semchonok@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] symmetrizing the model
Hi Dmitry, If you mean to create symmetry copies of an atomic model, it's basically the same command in ChimeraX as in Chimera, "sym", but with some small differences in the options and how you would specify them.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html
The easiest case is if the symmetry is already defined in the mmcif structure, e.g.:
open 1fav sym #1 assembly 1
... which by default will create a new model 2 that contains the assembly. There are lots of options, however, including whether it should be a new model or not, so you should look at the help page.
If the symmetry is not defined in the mmcif atomic structure file, you can specify symmetry group and parameters directly in the command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry
Example:
sym #1 C5 center 0,0,0
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2023, at 2:06 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues, A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application? I found the one for Chimera but not for ChimeraX. Many thanks. Sincerely, Dmitry
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Dmitry Semchonok -
Elaine Meng -
Tom Goddard