[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.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html>

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. 
Thanks,
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 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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