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

[Alexis Rohou]

Thanks Elaine!

Great - so now I'm using "measure center" to create markers with 0.0000001
radius at the center of my rings with specified modelId's. Then I have a
.pb file that specifies the pseudobonds to draw between markers and atoms.
That all seems to work pretty well, thanks!

Only little snag right now is I can't seem to get transparency working when
the color-spec in the .pb file is in the format rgba(). Setting the
transparency after opening the pb file using "transparency" works fine
though, so I'm not stuck.

Thanks again for the help.

Cheers,
Alexis

On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Here is the more detailed description of pseudobond file format:
>
> <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>
>
> > On Mar 6, 2020, at 9:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Alexis,
> > There is currently no option to specify a model number for the distance
> pseudobonds.  Typical usage doesn't usually require differentiating
> different sets of distances, but your case is atypical.
> >
> > If you really want to create several sets of pseudobonds as different
> models, it may be better to read each set in from a pseudobond input file.
> You'd have to create these text files (basically just lists of pairs of
> atom specifiers) named *.pb and then open them.
> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic>
> >
> > They will get sequential model numbers like other models that are
> opened.  Also you'd need to use other commands (size, style, color, ...) to
> change their appearance, not the Distances tool.
> >
> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html>
> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/style.html>
> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>
> >
> > 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 6, 2020, at 8:30 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
> >>
> >> 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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