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

[Alexis Rohou]

Thanks Elaine,

Distances work pretty well for this. I'm doing something like this, which
makes the marker so small that I can't see it:

measure center #1/A:841 at CG,CD2,CE2,CZ,CE1,CD1 mark true radius 0.0000001
model #1001
distance #1001 #1/A:840 at CD2

One question about the "distance" command. Is it possible to specify the
modelId of the distance model that is created? If not, I'd like to suggest
this as a useful addition - it would allow better scripting control over
showing labels etc (so you know what model # the distances have), and
creation of different groups of distances that could be manipulated
independently of each other.

Cheers,
Alexis



On Thu, Mar 5, 2020 at 2:23 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
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