[Chimera-users] info pivotting on a single atom

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 4 13:53:21 PDT 2013

Dear Christian,
If you use "select" instead of "cofr" does the command select the atom?  I.e., command:

select #3:700.A at N10

If it does not, there is something wrong with your specification.  

If it does, but the cofr command still doesn't work to put the center of rotation there, I have no idea about what could be happening.  Your command seems correct.

You could use menu: Help... Report a Bug, include short description with the cofr command that you tried and also attach your PDB file or a Chimera session file (because we can't fix a bug unless we can reproduce it).  Also include your email address to get feedback about what happens with your bug report. 
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 4, 2013, at 1:29 AM, Christian Martinoli wrote:

> 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?
> thankyou,
> Christian

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