Create pbonds or distances in different groups
Hi ChimeraX Community, When I create pseudobonds or distance measurements between atoms in ChimeraX, all of the pseudobonds/distances are grouped together. Is there a way to organize them into separate groups or subgroups so that I can modify their properties (e.g., color, radius, labels) independently? Thanks for your help. Best, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.
Hi Kai, If you're using the "pbond" command, you can specify option "name model-name" and each different model name creates a separate model. (This command also has a "showDist" option to label with the distance.) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/pbond.html> If you're opening a pbond file, each file will create a separate model. <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 8, 2026, at 8:40 AM, Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX Community, When I create pseudobonds or distance measurements between atoms in ChimeraX, all of the pseudobonds/distances are grouped together. Is there a way to organize them into separate groups or subgroups so that I can modify their properties (e.g., color, radius, labels) independently? Thanks for your help. Best, Kai UT Southwestern Medical Center The future of medicine, today._
Thank you Elaine. That works. Can similar actions be done with the 'distance' command? Best, Kai ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, June 8, 2026 3:40 PM To: Kai Cai <Kai.Cai@UTSouthwestern.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Create pbonds or distances in different groups Hi Kai, If you're using the "pbond" command, you can specify option "name model-name" and each different model name creates a separate model. (This command also has a "showDist" option to label with the distance. ) <https: //urldefense. com/v3/__https: //rbvi. ucsf. edu/chimerax/docs/user/commands/pbond. html__;!!MznTZTSvDXGV0Co!D78ZFOjFAsKUMKacnGO-0p01XdhlaPkVb9wvRe6x5Wk9pYFB_2VTmRduepIU2O6Chbglu-EuznHQzW6MMuN8zJRa$> Hi Kai, If you're using the "pbond" command, you can specify option "name model-name" and each different model name creates a separate model. (This command also has a "showDist" option to label with the distance.) <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...> If you're opening a pbond file, each file will create a separate model. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/pseudob...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 8, 2026, at 8:40 AM, Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX Community, When I create pseudobonds or distance measurements between atoms in ChimeraX, all of the pseudobonds/distances are grouped together. Is there a way to organize them into separate groups or subgroups so that I can modify their properties (e.g., color, radius, labels) independently? Thanks for your help. Best, Kai UT Southwestern Medical Center The future of medicine, today._
________________________________ UT Southwestern Medical Center The future of medicine, today.
No, but you can just use "pbond" instead with "showDist true" mentioned in my previous message. You can see all the options of a command (distance, etc.) in the User Guide page, simply click the command link in the Log. In this copy on our website, you can see that "distance" does not have a "name" option: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> It is more of a pain but if you really wanted to use "distance" for some reason, you could create a bunch of distances with that command, which always makes a model named "distances"... and then rename their model (see Models panel for the model number) to something else, and then resume using "distance" again to make a new "distances" model, etc. etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 9, 2026, at 10:37 AM, Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you Elaine. That works. Can similar actions be done with the 'distance' command? Best, KaiFrom: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, June 8, 2026 3:40 PM To: Kai Cai <Kai.Cai@UTSouthwestern.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Create pbonds or distances in different groups Hi Kai, If you're using the "pbond" command, you can specify option "name model-name" and each different model name creates a separate model. (This command also has a "showDist" option to label with the distance.) <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...>
If you're opening a pbond file, each file will create a separate model. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/pseudob...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 8, 2026, at 8:40 AM, Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX Community, When I create pseudobonds or distance measurements between atoms in ChimeraX, all of the pseudobonds/distances are grouped together. Is there a way to organize them into separate groups or subgroups so that I can modify their properties (e.g., color, radius, labels) independently? Thanks for your help. Best, Kai UT Southwestern Medical Center The future of medicine, today._
UT Southwestern Medical Center The future of medicine, today._______________________________________________ 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/
Thank you Elaine! Best, Kai ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, June 9, 2026 1:55 PM To: Kai Cai <Kai.Cai@UTSouthwestern.edu> Cc: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Create pbonds or distances in different groups No, but you can just use "pbond" instead with "showDist true" mentioned in my previous message. You can see all the options of a command (distance, etc. ) in the User Guide page, simply click the command link in the Log. In this copy on our website, No, but you can just use "pbond" instead with "showDist true" mentioned in my previous message. You can see all the options of a command (distance, etc.) in the User Guide page, simply click the command link in the Log. In this copy on our website, you can see that "distance" does not have a "name" option: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...> It is more of a pain but if you really wanted to use "distance" for some reason, you could create a bunch of distances with that command, which always makes a model named "distances"... and then rename their model (see Models panel for the model number) to something else, and then resume using "distance" again to make a new "distances" model, etc. etc. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 9, 2026, at 10:37 AM, Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you Elaine. That works. Can similar actions be done with the 'distance' command? Best, KaiFrom: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, June 8, 2026 3:40 PM To: Kai Cai <Kai.Cai@UTSouthwestern.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Create pbonds or distances in different groups Hi Kai, If you're using the "pbond" command, you can specify option "name model-name" and each different model name creates a separate model. (This command also has a "showDist" option to label with the distance.) <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...>
If you're opening a pbond file, each file will create a separate model. <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/pseudob...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 8, 2026, at 8:40 AM, Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX Community, When I create pseudobonds or distance measurements between atoms in ChimeraX, all of the pseudobonds/distances are grouped together. Is there a way to organize them into separate groups or subgroups so that I can modify their properties (e.g., color, radius, labels) independently? Thanks for your help. Best, Kai UT Southwestern Medical Center The future of medicine, today._
UT Southwestern Medical Center The future of medicine, today._______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...
________________________________ UT Southwestern Medical Center The future of medicine, today.
participants (2)
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Elaine Meng -
Kai Cai