info pivotting on a single atom
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 Italy
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@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
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 On 2 October 2013 19:30, Elaine Meng <meng@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@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 Italy
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
participants (2)
-
Christian Martinoli -
Elaine Meng