Hi, I just started using ChimeraX and am confronted with how to do a simple task, namely, to placer a specific atom at the centre of the screen. What is the replacement for the command “centre” in Chimera? Thanks,
Mirek
Hi Mirek, You could try "view" with a specifier for the atom or residue of interest, e.g.
show :43 view :43 view :43@cb
https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#initial
Or, you could select the atom(s) or residue and then use menu Actions... Focus
https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions
Or, you could use the "center" mouse mode function that centers on whatever you click with the assigned button:
https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.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 Jan 31, 2024, at 3:21 PM, Cygler, Miroslaw via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I just started using ChimeraX and am confronted with how to do a simple task, namely, to placer a specific atom at the centre of the screen. What is the replacement for the command “centre” in Chimera? Thanks, Mirek
Hi Elaine, Thanks for a quick answer. The first two options do what I wanted. For the third option, assign the “centre’ function to mouse, I do not see this option in the right mouse menu. What am I missing? Best,
Mirek
On Jan 31, 2024, at 6:38 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing@usask.ca
Hi Mirek, You could try "view" with a specifier for the atom or residue of interest, e.g.
show :43 view :43 view :43@cb
Or, you could select the atom(s) or residue and then use menu Actions... Focus
Or, you could use the "center" mouse mode function that centers on whatever you click with the assigned button:
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 Jan 31, 2024, at 3:21 PM, Cygler, Miroslaw via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I just started using ChimeraX and am confronted with how to do a simple task, namely, to placer a specific atom at the centre of the screen. What is the replacement for the command “centre” in Chimera? Thanks, Mirek
Hi Mirek, It's one of the several modes that don't have an icon. IInstead of clicking the icon, you have to assign it with the "mousemode" command. E.g. to assign it to right mouse, command
mousemode right center
The larger table of functions in the "mousemode" help page lists all of them regardless of whether they have an icon.
I hope this helps, Elaine
On Jan 31, 2024, at 5:14 PM, Cygler, Miroslaw via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, Thanks for a quick answer. The first two options do what I wanted. For the third option, assign the “centre’ function to mouse, I do not see this option in the right mouse menu. What am I missing? Best,
Mirek
On Jan 31, 2024, at 6:38 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing@usask.ca
Hi Mirek, You could try "view" with a specifier for the atom or residue of interest, e.g.
show :43 view :43 view :43@cb
Or, you could select the atom(s) or residue and then use menu Actions... Focus
Or, you could use the "center" mouse mode function that centers on whatever you click with the assigned button:
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 Jan 31, 2024, at 3:21 PM, Cygler, Miroslaw via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I just started using ChimeraX and am confronted with how to do a simple task, namely, to placer a specific atom at the centre of the screen. What is the replacement for the command “centre” in Chimera? Thanks, Mirek
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/
Links to "mousemode" command help and the full table of modes:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functions
I meant to send this link before but mistakenly sent the Right Mouse toolbar one instead, sorry about that.
Elaine
On Jan 31, 2024, at 5:31 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Mirek, It's one of the several modes that don't have an icon. IInstead of clicking the icon, you have to assign it with the "mousemode" command. E.g. to assign it to right mouse, command
mousemode right center
The larger table of functions in the "mousemode" help page lists all of them regardless of whether they have an icon.
I hope this helps, Elaine
On Jan 31, 2024, at 5:14 PM, Cygler, Miroslaw via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Elaine, Thanks for a quick answer. The first two options do what I wanted. For the third option, assign the “centre’ function to mouse, I do not see this option in the right mouse menu. What am I missing? Best,
Mirek
On Jan 31, 2024, at 6:38 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing@usask.ca
Hi Mirek, You could try "view" with a specifier for the atom or residue of interest, e.g.
show :43 view :43 view :43@cb
Or, you could select the atom(s) or residue and then use menu Actions... Focus
Or, you could use the "center" mouse mode function that centers on whatever you click with the assigned button:
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 Jan 31, 2024, at 3:21 PM, Cygler, Miroslaw via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I just started using ChimeraX and am confronted with how to do a simple task, namely, to placer a specific atom at the centre of the screen. What is the replacement for the command “centre” in Chimera? Thanks, Mirek
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 (2)
-
Cygler, Miroslaw -
Elaine Meng