how to turn molecule centering a specific atom in ChimeraX
Hi, I was trying to turn molecule around specific atom. Since I am a beginner of ChimeraX, I would like to have some working examples in the command line. Without it, I have difficulties in applying the usage as appeared in the user guide. In PyMOL, mouse middle button click on a atom sets the centering on the atom then use rotate command. I appreciate all the supports provided. Thank you. Inchul
Hi Inchul, You can select an atom with Ctrl-click and then use menu: Actions... Set Pivot. You can also set the center of rotation to the selected atom with command: cofr sel ...which is exactly the same as using the menu item mentioned above, and in fact using the menu will show that command in the Log. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cofr.html> Or you can name the atom(s) directly instead of selecting it, for example, command: cofr #1/A:253@ca ... model 1 chain A residue 253 atom name CA. Command-line atom specification is described here, with several examples: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> Or, if you want something more similar to Pymol and you often want to change the center of rotation, you can assign a mouse button to change the center of rotation to the atom that is clicked with that button. In the "Right Mouse" tab of Toolbar icons across the top of the window, there is "set pivot" icon which looks like a red circle with an arrow going around it and a red dot in the middle. You can click that to assign the right mouse button to that function. The mouse-mode icons and their meanings are given here. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> Or, you can assign other mouse buttons (not just right button) alone or in combination with Ctrl, Shift, etc. to that function using the "mousemode" command. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 7, 2020, at 1:46 PM, Shin Inchul <Inchul.Shin@utsa.edu> wrote:
Hi,
I was trying to turn molecule around specific atom. Since I am a beginner of ChimeraX, I would like to have some working examples in the command line. Without it, I have difficulties in applying the usage as appeared in the user guide. In PyMOL, mouse middle button click on a atom sets the centering on the atom then use rotate command.
I appreciate all the supports provided.
Thank you. Inchul
If those were not enough options you can also rotate about a specific atom directly with the turn command turn y 45 center #1/A:253@CA Tom
On Jul 7, 2020, at 3:15 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Inchul, You can select an atom with Ctrl-click and then use menu: Actions... Set Pivot.
You can also set the center of rotation to the selected atom with command:
cofr sel
...which is exactly the same as using the menu item mentioned above, and in fact using the menu will show that command in the Log. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cofr.html>
Or you can name the atom(s) directly instead of selecting it, for example, command:
cofr #1/A:253@ca
... model 1 chain A residue 253 atom name CA. Command-line atom specification is described here, with several examples: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
Or, if you want something more similar to Pymol and you often want to change the center of rotation, you can assign a mouse button to change the center of rotation to the atom that is clicked with that button. In the "Right Mouse" tab of Toolbar icons across the top of the window, there is "set pivot" icon which looks like a red circle with an arrow going around it and a red dot in the middle. You can click that to assign the right mouse button to that function. The mouse-mode icons and their meanings are given here. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>
Or, you can assign other mouse buttons (not just right button) alone or in combination with Ctrl, Shift, etc. to that function using the "mousemode" command. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 7, 2020, at 1:46 PM, Shin Inchul <Inchul.Shin@utsa.edu> wrote:
Hi,
I was trying to turn molecule around specific atom. Since I am a beginner of ChimeraX, I would like to have some working examples in the command line. Without it, I have difficulties in applying the usage as appeared in the user guide. In PyMOL, mouse middle button click on a atom sets the centering on the atom then use rotate command.
I appreciate all the supports provided.
Thank you. Inchul
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
It works! Thank you, Elanie and Tom!! Inchul ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, July 7, 2020 5:29 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Cc: Shin Inchul <Inchul.Shin@utsa.edu> Subject: [EXTERNAL] Re: [chimerax-users] how to turn molecule centering a specific atom in ChimeraX **EXTERNAL EMAIL** This email originated outside of The University of Texas at San Antonio. Please exercise caution when clicking on links or opening attachments. If those were not enough options you can also rotate about a specific atom directly with the turn command turn y 45 center #1/A:253@CA Tom
On Jul 7, 2020, at 3:15 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Inchul, You can select an atom with Ctrl-click and then use menu: Actions... Set Pivot.
You can also set the center of rotation to the selected atom with command:
cofr sel
...which is exactly the same as using the menu item mentioned above, and in fact using the menu will show that command in the Log. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcofr.html&data=02%7C01%7CInchul.Shin%40utsa.edu%7C67b2f619e9c848c7a39d08d822c5355a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C1%7C637297577695914550&sdata=ueMS6HFMOe853jBiiAWmtDp7KjjCMMJyg93EsZfDoww%3D&reserved=0>
Or you can name the atom(s) directly instead of selecting it, for example, command:
cofr #1/A:253@ca
... model 1 chain A residue 253 atom name CA. Command-line atom specification is described here, with several examples: <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fatomspec.html&data=02%7C01%7CInchul.Shin%40utsa.edu%7C67b2f619e9c848c7a39d08d822c5355a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C1%7C637297577695914550&sdata=0hqXrLi26Vj05Y76v9X0ShxjJOR5BUElDnqUt1BQnQM%3D&reserved=0>
Or, if you want something more similar to Pymol and you often want to change the center of rotation, you can assign a mouse button to change the center of rotation to the atom that is clicked with that button. In the "Right Mouse" tab of Toolbar icons across the top of the window, there is "set pivot" icon which looks like a red circle with an arrow going around it and a red dot in the middle. You can click that to assign the right mouse button to that function. The mouse-mode icons and their meanings are given here. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fmousemodes.html&data=02%7C01%7CInchul.Shin%40utsa.edu%7C67b2f619e9c848c7a39d08d822c5355a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C1%7C637297577695914550&sdata=mghSXe9gUQYJ70P%2FjmzZ%2B%2FtJkyOW8ubYCwDq8hHS6rs%3D&reserved=0>
Or, you can assign other mouse buttons (not just right button) alone or in combination with Ctrl, Shift, etc. to that function using the "mousemode" command. <https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fui.html%23mousemode&data=02%7C01%7CInchul.Shin%40utsa.edu%7C67b2f619e9c848c7a39d08d822c5355a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C1%7C637297577695914550&sdata=F%2FZnkJi7Q1%2BsNq6scvgKG5cc7Z57fn4AmP16%2BVs%2BJX0%3D&reserved=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 Jul 7, 2020, at 1:46 PM, Shin Inchul <Inchul.Shin@utsa.edu> wrote:
Hi,
I was trying to turn molecule around specific atom. Since I am a beginner of ChimeraX, I would like to have some working examples in the command line. Without it, I have difficulties in applying the usage as appeared in the user guide. In PyMOL, mouse middle button click on a atom sets the centering on the atom then use rotate command.
I appreciate all the supports provided.
Thank you. Inchul
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimerax-users&data=02%7C01%7CInchul.Shin%40utsa.edu%7C67b2f619e9c848c7a39d08d822c5355a%7C3a228dfbc64744cb88357b20617fc906%7C0%7C1%7C637297577695914550&sdata=I7bCNJ%2B6p68e5GhrtrA95mk9n3cyWD1AsVIeSLh2wu8%3D&reserved=0
participants (3)
-
Elaine Meng -
Shin Inchul -
Tom Goddard