[Chimera-users] Finding and depicting intermolecular interactions

Elaine Meng meng at cgl.ucsf.edu
Sun Mar 27 10:21:03 PDT 2016

Hi Henrique,
Sorry, although there is a FindHBond tool,  there is nothing to automatically find halogen bonds or pi stacking in Chimera.  You would have to find possible interactions by eye and then measure distances between specific pairs of atoms.  Measuring the distance also shows dashed lines.

You can measure distances by any of the following:

(A) Ctrl-click one atom to select, Shift-Ctrl-doubleclick second atom to add to selection and  at the same time show a pop-up menu including Show Distance

(B) Ctrl-click one atom to select, Shift-Ctrl-click second atom to add to selection.  Now there are 2 atoms selected and you can click “Create” in the Distances tool (in menu under Tools… Structure Analysis) to measure the distance.  This tool also has options to change the appearance of the dashed lines.

(C) “distance” command including atom specifiers, or including “sel” if the two atoms are already selected as in (B)

Another complication is that distance measurements are only between atomic centers.  If you want to measure a distance to the center of some ring, you would first need to put a pseudoatom at that point, for example by selecting all the ring atoms and then using a command something like: 
measure center sel mark true radius 0.3 color cyan

The “mark true” part says to create a new model with one pseudoatom.  You can close or hide that model from the Model Panel (see Favorites menu), similar to any other structure that you open.

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 Mar 27, 2016, at 8:40 AM, Henrique C. S. Junior <henriquecsj at gmail.com> wrote:

> Dear Chimera list,
> I'm Interested in finding and showing halogen bonds and pi stackings. Is that possible?
> Attached is an example made using Schrodinger's Maestro.
> Thanks in advance

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