projecting full model from monomer
Dear colleagues,
I have a monomer with biomt information that describes the full model. To see the full model, I use the command sym when opening the monomer in Chimera.
Could you please prompt the correspondent command in ChimeraX to project the complete model in ChimeraX based on the information stored in the monomer?
Thank you
Kind regards, Dmitry
Hi Dmitry, It is also the "sym" command, but you need to say which assembly you want, and it depends on the specific structure what assemblies are available. Or instead of running the command directly, when you first open the structure it may list the assemblies in the Log and you can just click on it (in the Log) which will run the command. For details of the command, see the help:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#assembly
Or you can just enter command "help sym" to see the same page included with your download.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 12, 2023, at 11:21 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues,
I have a monomer with biomt information that describes the full model. To see the full model, I use the command sym when opening the monomer in Chimera.
Could you please prompt the correspondent command in ChimeraX to project the complete model in ChimeraX based on the information stored in the monomer?
Thank you
Kind regards, Dmitry
Thank you, Elaine,
Could you please also prompt the analogue command for the ChimeraX for sym #2 group #1 in chimera? When I run this command in ChimeraX I get an error - Expected a keyword
Thank you.
Sincerely, Dmitry
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: 12 November 2023 19:28 To: Dmitry Semchonok semchonok@gmail.com Cc: ChimeraX chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] projecting full model from monomer
Hi Dmitry, It is also the "sym" command, but you need to say which assembly you want, and it depends on the specific structure what assemblies are available. Or instead of running the command directly, when you first open the structure it may list the assemblies in the Log and you can just click on it (in the Log) which will run the command. For details of the command, see the help:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#assembly
Or you can just enter command "help sym" to see the same page included with your download.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 12, 2023, at 11:21 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues,
I have a monomer with biomt information that describes the full model. To see the full model, I use the command sym when opening the monomer in Chimera.
Could you please prompt the correspondent command in ChimeraX to project the complete model in ChimeraX based on the information stored in the monomer?
Thank you
Kind regards, Dmitry
Hi Dmitry, If you would look at the help page, you would see there is no "group" option in ChimeraX "sym" command.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html
From looking at it myself, the option to use the symmetry from another model is "symmetry", so try this:
sym #2 symmetry #1
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 12, 2023, at 11:35 AM, Dmitry Semchonok Semchonok@gmail.com wrote:
Thank you, Elaine,
Could you please also prompt the analogue command for the ChimeraX for sym #2 group #1 in chimera? When I run this command in ChimeraX I get an error - Expected a keyword
Thank you.
Sincerely, Dmitry
From: Elaine Meng meng@cgl.ucsf.edu Sent: 12 November 2023 19:28 To: Dmitry Semchonok semchonok@gmail.com Cc: ChimeraX chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] projecting full model from monomer
Hi Dmitry, It is also the "sym" command, but you need to say which assembly you want, and it depends on the specific structure what assemblies are available. Or instead of running the command directly, when you first open the structure it may list the assemblies in the Log and you can just click on it (in the Log) which will run the command. For details of the command, see the help:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#assembly
Or you can just enter command "help sym" to see the same page included with your download.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 12, 2023, at 11:21 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues,
I have a monomer with biomt information that describes the full model. To see the full model, I use the command sym when opening the monomer in Chimera.
Could you please prompt the correspondent command in ChimeraX to project the complete model in ChimeraX based on the information stored in the monomer?
Thank you
Kind regards, Dmitry
Dear Elaine,
Many thanks! I really appreciate your help and advice.
Sincerely, Dmitry
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: 13 November 2023 17:47 To: Dmitry Semchonok Semchonok@gmail.com Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] projecting full model from monomer
Hi Dmitry, If you would look at the help page, you would see there is no "group" option in ChimeraX "sym" command.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html
From looking at it myself, the option to use the symmetry from another model is "symmetry", so try this:
sym #2 symmetry #1
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 12, 2023, at 11:35 AM, Dmitry Semchonok Semchonok@gmail.com wrote:
Thank you, Elaine,
Could you please also prompt the analogue command for the ChimeraX for sym #2 group #1 in chimera? When I run this command in ChimeraX I get an error - Expected a keyword
Thank you.
Sincerely, Dmitry
From: Elaine Meng meng@cgl.ucsf.edu Sent: 12 November 2023 19:28 To: Dmitry Semchonok semchonok@gmail.com Cc: ChimeraX chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] projecting full model from monomer
Hi Dmitry, It is also the "sym" command, but you need to say which assembly you want, and it depends on the specific structure what assemblies are available. Or instead of running the command directly, when you first open the structure it may list the assemblies in the Log and you can just click on it (in the Log) which will run the command. For details of the command, see the help:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#assembly
Or you can just enter command "help sym" to see the same page included with your download.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 12, 2023, at 11:21 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues,
I have a monomer with biomt information that describes the full model. To see the full model, I use the command sym when opening the monomer in Chimera.
Could you please prompt the correspondent command in ChimeraX to project the complete model in ChimeraX based on the information stored in the monomer?
Thank you
Kind regards, Dmitry
participants (2)
-
Dmitry Semchonok
-
Elaine Meng