Dear Christian, If you use "select" instead of "cofr" does the command select the atom? I.e., command: select #3:700.A@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@N10
the syntax seems correct but still the actual center of rotation is somewhere else
any idea about? thankyou, Christian