Begin forwarded message:
From: Yanhe Zhao <yanhezhao1990@gmail.com> Subject: choose the rotation center Date: February 1, 2022 at 1:02:12 PM PST To: chimera-users-owner@cgl.ucsf.edu
Hello there,
I want to fixed the center for my rotation but have two questions here: 1, how I easily read out the xyz coordinate of the point I want to use as center? 2, as attached, what the xyz sequence here, xyz from top to bottom?
Thanks and appreciate for your help! Yanhe
Hi Yanhe, easy question first (2) Yes As for (1), if you just want to use the position of some atom (or approximate center of some group of atoms), you don't need to figure it out and then enter numbers in the dialog. Instead you can just either (A) select the atom(s) and use the menu: Actions... Set Pivot <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#actpivot> - OR - (B) use the "cofr" command <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html> ...and specify one or more atoms, for example cofr #1:50.A@CA cofr #1:50.A cofr sel ...where "sel" means currently selected atoms. However, if you have calculated X,Y,Z that you want as the center using some other method you can also specify them with the "cofr" command: cofr 5.5,14.2,15.0 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
From: Yanhe Zhao <yanhezhao1990@gmail.com> Subject: choose the rotation center Date: February 1, 2022 at 1:02:12 PM PST To: chimera-users-owner@cgl.ucsf.edu
Hello there,
I want to fixed the center for my rotation but have two questions here: 1, how I easily read out the xyz coordinate of the point I want to use as center? 2, as attached, what the xyz sequence here, xyz from top to bottom?
Thanks and appreciate for your help! Yanhe <Screenshot from 2022-02-01 14-53-52.png>
Dear Elaine, Thanks a lot for your help. It works. Thanks and cheers, Yanhe Elaine Meng <meng@cgl.ucsf.edu> 于2022年2月1日周二 15:18写道：
Hi Yanhe, easy question first (2) Yes
As for (1), if you just want to use the position of some atom (or approximate center of some group of atoms), you don't need to figure it out and then enter numbers in the dialog. Instead you can just either
(A) select the atom(s) and use the menu: Actions... Set Pivot <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#actpivot>
- OR -
(B) use the "cofr" command <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html>
...and specify one or more atoms, for example
cofr #1:50.A@CA cofr #1:50.A cofr sel
...where "sel" means currently selected atoms. However, if you have calculated X,Y,Z that you want as the center using some other method you can also specify them with the "cofr" command:
cofr 5.5,14.2,15.0
I hope this helps,
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
From: Yanhe Zhao <yanhezhao1990@gmail.com> Subject: choose the rotation center Date: February 1, 2022 at 1:02:12 PM PST To: chimera-users-owner@cgl.ucsf.edu
Hello there,
I want to fixed the center for my rotation but have two questions here: 1, how I easily read out the xyz coordinate of the point I want to use
as center?
2, as attached, what the xyz sequence here, xyz from top to bottom?
Thanks and appreciate for your help! Yanhe <Screenshot from 2022-02-01 14-53-52.png>
participants (3)
-
Elaine Meng -
Eric Pettersen -
Yanhe Zhao