[chimerax-users] pseudobond between atom and center of a ring

[Elaine Meng]

Hi Alexis,
You could use "measure center" with "mark true" to add dummy atoms at the centers of rings.  We are working on axes/planes/centroids functionality similar to that available in Chimera, but it is not yet available.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#center>

Then one way to draw a dashed line is to add a distance monitor between any pair of atoms, then edit line appearance in the Distances tool (in menu under Tools... Structure Analysis).  You can hide the distance labels by unchecking the "shown" checkbox (under the eye icon) for the labels model in the Model Panel. You may need to use the disclosure triangle to show the "labels" submodel of "distances" model.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/distances.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html>

I believe you have to show the atoms on both ends for the pseudobond to remain visible, however.  If you hide one atom, that hides the pseudobond.  You could make the atom's radius small (see "size") or make it 100% transparent (see "transparency"), e.g.

transparency sel 100 target a

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html>
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.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 Mar 5, 2020, at 1:58 PM, Alexis Rohou <a.rohou at gmail.com> wrote:
> 
> Hi all,
> 
> Looking for ideas on how to achieve the following, if possible: 
> 
> I'd like to draw lines to represent favorable ring-ring stacking interactions (lines between the center of two arene rings), ring-ring edge-to-face interactions (between one atom of one ring and the center of the other ring), and between a regular atom (not part of a ring) and the center of an arene ring.
> 
> So I'm guess what I'm looking for is a way to:
> 1. compute the center coordinates of a ring
> 2. place an invisible atom there
> 3. create a pseudobond between this virtual atom and other atoms/virtual atoms
> 
> Any suggestions as to how I could achieve this?
> 
> Cheers,
> Alexis