Dear team, Classic Chimera had a command to turn off specific models, allowing manipulation of the other model(s). What is the command for that in ChimeraX? ChatGPT gave as answer “model toggle off #1” but that appears to be wrong. Thank you, Peter ---------------------------------- Peter M.J. Burgers Marvin Brennecke Professor of Biological Chemistry Department of Biochemistry and Molecular Biophysics Washington University School of Medicine BOX 8231 660 South Euclid Saint Louis, MO 63110 E-Mail: burgers@wustl.edu<applewebdata://1B940EF6-0122-4328-902B-DCB358A99492/burgers@biochem.wustl.edu> PH (314) 362-3872 (office) 286-2554 (lab) FAX (314) 362-7183 http://biochem.wustl.edu/~burgersw3/ ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Hi Peter, This works differently in ChimeraX. There is no "inactivation for motion" of models in ChimeraX. Instead you use different "mouse modes," function assignments to touchpad or mouse that translate or rotate only the clicked model or the selected models or atoms. Different mouse modes can be assigned to right mouse button or touchpad equivalent by clicking an icon in the Right Mouse tab of the toolbar across the top, and to other buttons (alone or in combination with modifier keys like Shift) using the "mousemode" command. For a more detailed explanation, see "selective manipulation" and links therein: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> Scanning the User Guide index is definitely recommended before using chatGPT... the latter frequently makes up ridiculously wrong instructions that will waste your time. <https://rbvi.ucsf.edu/chimerax/docs/user/index.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 Mar 21, 2025, at 10:16 AM, Burgers, Peter via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear team, Classic Chimera had a command to turn off specific models, allowing manipulation of the other model(s). What is the command for that in ChimeraX? ChatGPT gave as answer “model toggle off #1” but that appears to be wrong. Thank you, Peter
Thank you, Elaine. The mouse modes and the toolbar are pretty easy to use. But does this mean that there is no way to de-activate all models? Peter On 3/21/25, 3:30 PM, "Elaine Meng" <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Peter, This works differently in ChimeraX. There is no "inactivation for motion" of models in ChimeraX. Instead you use different "mouse modes," function assignments to touchpad or mouse that translate or rotate only the clicked model or the selected models or atoms. Different mouse modes can be assigned to right mouse button or touchpad equivalent by clicking an icon in the Right Mouse tab of the toolbar across the top, and to other buttons (alone or in combination with modifier keys like Shift) using the "mousemode" command. For a more detailed explanation, see "selective manipulation" and links therein: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective;> Scanning the User Guide index is definitely recommended before using chatGPT... the latter frequently makes up ridiculously wrong instructions that will waste your time. <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> <https://rbvi.ucsf.edu/chimerax/docs/user/index.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 Mar 21, 2025, at 10:16 AM, Burgers, Peter via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear team, Classic Chimera had a command to turn off specific models, allowing manipulation of the other model(s). What is the command for that in ChimeraX? ChatGPT gave as answer “model toggle off #1” but that appears to be wrong. Thank you, Peter
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Hi Peter, As I understand it, there is no "inactivation for motion" of models in ChimeraX. I.e. the concept does not exist. You could set all your mouse buttons to modes that do not move the models, I suppose. 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 Mar 23, 2025, at 7:23 PM, Burgers, Peter via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you, Elaine. The mouse modes and the toolbar are pretty easy to use. But does this mean that there is no way to de-activate all models? Peter
On 3/21/25, 3:30 PM, "Elaine Meng" <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hi Peter, This works differently in ChimeraX. There is no "inactivation for motion" of models in ChimeraX.
Instead you use different "mouse modes," function assignments to touchpad or mouse that translate or rotate only the clicked model or the selected models or atoms. Different mouse modes can be assigned to right mouse button or touchpad equivalent by clicking an icon in the Right Mouse tab of the toolbar across the top, and to other buttons (alone or in combination with modifier keys like Shift) using the "mousemode" command.
For a more detailed explanation, see "selective manipulation" and links therein: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective;>
Scanning the User Guide index is definitely recommended before using chatGPT... the latter frequently makes up ridiculously wrong instructions that will waste your time. <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> <https://rbvi.ucsf.edu/chimerax/docs/user/index.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 Mar 21, 2025, at 10:16 AM, Burgers, Peter via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear team, Classic Chimera had a command to turn off specific models, allowing manipulation of the other model(s). What is the command for that in ChimeraX? ChatGPT gave as answer “model toggle off #1” but that appears to be wrong. Thank you, Peter
Hi Peter, If your issue is accidentally messing up a position that you wanted to keep, maybe you can use "view name" to save the position so that you can easily return to it. If you save a session, it includes all the named views that you saved. Also, if you just want to get back to the positions of the models when the session was saved, there is an automatically generated view named "session-start" -- see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> The named views in ChimeraX are analogous to the "positions" we had in Chimera. I hope this helps, Elaine
On Mar 24, 2025, at 8:21 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Peter, As I understand it, there is no "inactivation for motion" of models in ChimeraX. I.e. the concept does not exist.
You could set all your mouse buttons to modes that do not move the models, I suppose. 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 Mar 23, 2025, at 7:23 PM, Burgers, Peter via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you, Elaine. The mouse modes and the toolbar are pretty easy to use. But does this mean that there is no way to de-activate all models? Peter
On 3/21/25, 3:30 PM, "Elaine Meng" <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hi Peter, This works differently in ChimeraX. There is no "inactivation for motion" of models in ChimeraX.
Instead you use different "mouse modes," function assignments to touchpad or mouse that translate or rotate only the clicked model or the selected models or atoms. Different mouse modes can be assigned to right mouse button or touchpad equivalent by clicking an icon in the Right Mouse tab of the toolbar across the top, and to other buttons (alone or in combination with modifier keys like Shift) using the "mousemode" command.
For a more detailed explanation, see "selective manipulation" and links therein: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective;>
Scanning the User Guide index is definitely recommended before using chatGPT... the latter frequently makes up ridiculously wrong instructions that will waste your time. <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> <https://rbvi.ucsf.edu/chimerax/docs/user/index.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 Mar 21, 2025, at 10:16 AM, Burgers, Peter via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear team, Classic Chimera had a command to turn off specific models, allowing manipulation of the other model(s). What is the command for that in ChimeraX? ChatGPT gave as answer “model toggle off #1” but that appears to be wrong. Thank you, Peter
Dear Elaine, Thanks. This helps with keeping a position. Peter On 3/24/25, 10:30 AM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote: Hi Peter, If your issue is accidentally messing up a position that you wanted to keep, maybe you can use "view name" to save the position so that you can easily return to it. If you save a session, it includes all the named views that you saved. Also, if you just want to get back to the positions of the models when the session was saved, there is an automatically generated view named "session-start" -- see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> The named views in ChimeraX are analogous to the "positions" we had in Chimera. I hope this helps, Elaine > On Mar 24, 2025, at 8:21 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote: > > Hi Peter, > As I understand it, there is no "inactivation for motion" of models in ChimeraX. I.e. the concept does not exist. > > You could set all your mouse buttons to modes that do not move the models, I suppose. > 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 Mar 23, 2025, at 7:23 PM, Burgers, Peter via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: >> >> Thank you, Elaine. >> The mouse modes and the toolbar are pretty easy to use. But does this mean that there is no way to de-activate all models? >> Peter >> >> On 3/21/25, 3:30 PM, "Elaine Meng" <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >> >> >> Hi Peter, >> This works differently in ChimeraX. There is no "inactivation for motion" of models in ChimeraX. >> >> >> Instead you use different "mouse modes," function assignments to touchpad or mouse that translate or rotate only the clicked model or the selected models or atoms. Different mouse modes can be assigned to right mouse button or touchpad equivalent by clicking an icon in the Right Mouse tab of the toolbar across the top, and to other buttons (alone or in combination with modifier keys like Shift) using the "mousemode" command. >> >> >> For a more detailed explanation, see "selective manipulation" and links therein: >> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#selective;> >> >> >> Scanning the User Guide index is definitely recommended before using chatGPT... the latter frequently makes up ridiculously wrong instructions that will waste your time. >> <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> <https://rbvi.ucsf.edu/chimerax/docs/user/index.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 Mar 21, 2025, at 10:16 AM, Burgers, Peter via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Dear team, >>> Classic Chimera had a command to turn off specific models, allowing manipulation of the other model(s). >>> What is the command for that in ChimeraX? >>> ChatGPT gave as answer “model toggle off #1” but that appears to be wrong. >>> Thank you, >>> Peter >> > ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
participants (2)
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Burgers, Peter -
Elaine Meng