[Chimera-users] Question regarding bond angle

[Elaine Meng]

Hi Prathvi,
Well, the trivial answer is yes, simply moving C relative to A-B will change that angle ... but I'm guessing you meant some single command to create a specific angle.  In that case, sorry no, there is no command to do that.

The following assumes that C and A-B are not in the same molecule.  If they are in the same molecule it is even more complicated because you don't want to end up with a ridiculous strained conformation of that molecule.

In Chimera: 
(A) If C is in a different model than A-B (i.e. opened from two different pdb files or separated after opening a single model with the "split" command), you can move one model with the mouse while the other is frozen in place, and iteratively re-measure the angle after moving. Models can be frozen (deactivated for motion) and re-activated (made movable with mouse again) as described here:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
(B) or, if you want to keep them in the same model, you can move only the selected atoms using the Movement Mouse Mode tool (in menu under Tools... Structure Editing)
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode.html>

 It may be difficult to achieve what you want, however, with manual movements.

Alternatively, you could try calculating (just using trigonometry) the needed translation of C relative to A-B to get the angle you want, and then apply it with the "move" command.

ChimeraX also allows manual movements or specific translation amounts, but details of how to do it are different.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 13, 2022, at 11:58 PM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi again Elaine,
> Is there a way in chimera or chimeraX to change the angle between three atoms A,B,C where atoms A & B are covalently bonded to each other but neither A nor B is bonded to C ?
>