[Chimera-users] Measuring angles between atoms pairs

[Elaine Meng]

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 at ca:4.a at ca:6.b at 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
>