[Chimera-users] Measuring angles between atoms pairs

Elaine Meng meng at cgl.ucsf.edu
Wed Sep 26 10:52:06 PDT 2012

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:
How to specify atoms by name:

I can't answer the Python part, except that there are some basic scripting instructions here:

I hope this helps,
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

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