[Chimera-users] info pivotting on a single atom

Christian Martinoli christian.martinoli at unipv.it
Fri Oct 4 01:29:37 PDT 2013

Dear Elaine,
still, also with your suggestions, I could not overcome the problem.
Since I need to write a script, I need to use just command lines not the
graphic interface (where the pivot selection is working). Using cofr i
expected that the selected atom would have taken as pivot of the entire
molecule, which in my case is not.
this is the exact line I 'm using.

cofr #3:700.A at N10

the syntax seems correct but still the actual center of rotation is
somewhere  else

any idea about?

On 2 October 2013 19:30, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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

Christian Martinoli
University Of Pavia
Dept. of Biology and Biotechnology "Lazzaro Spallanzani"
Structural Biology Lab.
Via Ferrata 1, 27100 Pavia
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