[Chimera-users] Finding and depicting intermolecular interactions

Henrique C. S. Junior henriquecsj at gmail.com
Sun Mar 27 11:03:14 PDT 2016

Thank you for your nice reply, Elaine.
Maybe this is a feature for some time in the future? ;-)

2016-03-27 14:21 GMT-03:00 Elaine Meng <meng at cgl.ucsf.edu>:

> 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.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances
> >
> (C) “distance” command including atom specifiers, or including “sel” if
> the two atoms are already selected as in (B)
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
> 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
> -----
> 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

*Henrique C. S. Junior*
Químico Industrial - UFRRJ
Mestrando em Química Inorgânica - UFRRJ
Centro de Processamento de Dados - PMP
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