Hi Yasser, It does not matter if the atoms are bonded or not. You could name any 3 or 4 atoms (for "valence" or "torsion" type of angle), for example with command: angle :2.a@ca:4.a@ca:6.b@ca (angle formed by three CA atoms: in residue 2 chain A, residue 4 chain A, residue 6 chain B) Or, instead of using names, you could select atoms (in order) with the mouse and then use: angle sel Angle command: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html> How to specify atoms by name: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#subcats> I can't answer the Python part, except that there are some basic scripting instructions here: <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> 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 Sep 26, 2012, at 11:04 AM, Yasser Almeida Hernandez wrote:
Dear Chimerians...
I'm running an analysis about H-bonds geometries in several models.
I need to measure the distance of a H-bond and the angle formed with a third atom bonded to one of the H-bond atoms. How could I do that in a python IDLE/script?
In a more general way, how could I measure the angle between three atoms linked by a bond o pseudobond?
Thanks in advance
Yasser