[Chimera-users] info pivotting on a single atom

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 2 10:30:28 PDT 2013


Dear Christian,
The center of rotation is in 3D, not 2D.  I"m not sure what you are doing, but some ways to set the center of rotation to a single atom are:

(1) select atom, choose menu: Actions... Set Pivot
(2) select atom, use command: cofr sel
(3) or for command-line only (as in a script), name the atom directly in the command, e.g.: 
cofr #0:25.a at ca

Even if you accidentally specified more than one atom in the command, it would still use the center of the bounding sphere of the atom(s) for 3D rotation.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html>

Maybe the issue is in your subsequent rotation commands. The "turn" "rock" and "roll" commands all take an axis specification, which could be simply x, y, z, or something more complicated to indicate any possible direction.  Also, you can specify center of rotation directly within those commands instead of separately with the "cofr" command.  See their manual pages for more information.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 2, 2013, at 9:51 AM, Christian Martinoli wrote:

> dear all,
> I have troubles in setting the center of rotation on a single atom of my model. i'm working with the command line to build up a short clip at the end.what i would need is pivotting the whole model on the three axes, rather than in 2D as seems work with cofr command. any help?
> Thanks in advance
> Christian




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