[Chimera-users] pi-pi interactions

[Elaine Meng]

Hi Ann,
Welcome to Chimera! Definitely this list is the right place to ask whether Chimera can do something, or if so, how to do it. (I changed the “subject” in case other people search for this topic later)

However, Chimera doesn’t have anything specific for pi-pi interaction analysis. You can do various steps of a more manual analysis, but instead you might prefer to use a different program that does the analysis more automatically.

In Chimera,

(A) you can select aromatic rings, e.g. commands like:  
select aromatic ring
  (select all aromatic rings)
select :15.A & aromatic ring
  (select aromatic ring(s) of residue 15 in chain A)
… or by hand-selecting with Shift-Ctrl-click on the atoms of a ring in the 3D structure
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

(B) if you selected the atoms of a ring, you can calculate its plane and/or centroid (Tools… Structure Analysis… Axes/Planes/Centroids or “define” command)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>

(C) you can calculate distances between centroids and angles between planes (using Axes/Planes/Centroids graphical interface or “distance” and “angle” commands).  You’d still have to decide what distances and angles correspond to a pi-pi interaction.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

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

> On Dec 12, 2018, at 9:59 AM, Xhoela Bame <xhoelabame at yahoo.com> wrote:
> 
> Hello,
>  I am new in using chimera and new in this group. I was wondering if I can ask questions related to the techniques here. 
> I want to study the pi-pi interactions between a protein and its ligand. Any suggestions on how to do that using chimera?
> Thanks!
> Ann