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

[Tom Goddard]

Hi Alexis,

  You could place markers and link them with the Markers tab of the toolbar.  Using the place marker at Point mode then the Move mode you could position it by hand at the center of a ring or on an atom.  If you prefer to use calculated positions you could use the "measure center" command on selected atoms of a ring, then use the marker command to place a marker exactly at the reported position.

	https://www.cgl.ucsf.edu/chimerax/docs/user/tools/markerplacement.html <https://www.cgl.ucsf.edu/chimerax/docs/user/tools/markerplacement.html>

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#center <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#center>

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html>

  Tom


> 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
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