[Chimera-users] Displaying Labels without displaying Atoms

Nicholas Hyman nicholas.j.hyman at vanderbilt.edu
Thu Jun 23 16:16:46 PDT 2016

Thank you so much this was incredibly helpful!

*Nicholas Hyman*
Vanderbilt University, Computer Science and Chemistry, Class of 2018
(770) 314-9270 | nicholas.j.hyman at vanderbilt.edu

On Thu, Jun 23, 2016 at 5:54 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Nicholas,
> Several pseudobond “attributes” like whether they depend on atom display
> and their linewidth, color, label text etc. can be controlled with the
> “setattr” command.  Some of the attributes are at the level of the
> pseudobond group, such as all distance measurements, whereas others can be
> changed for individual pseudobonds.   How you can tell which of those
> applies and the name of the attribute for use with the “setattr” command is
> by selecting any pseudobond, showing the Selection Inspector (e.g. by
> clicking the green magnifying glass icon at the lower right corner), and
> then mousing over the entries in the dialog when inspecting “pseudobond”
> or “pseudobond group.”  The pop-up balloon help will give the attribute
> name and some information about its possible values. Or instead of in the
> Selection Inspector, this lookup can also be done in the pseudobond group
> attributes dialog opened with the “attributes…” function in the Pseudobond
> Panel  (menu:  Tools… General Controls… Pseudobond Panel).
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/pbattrib.html>
> I gave you the long answer above so you could understand how to change
> several things about pseudobonds with “setattr” …. the short answer is  a
> command something like:
> setattr p display 1
> … as shown in the aforementioned balloon help, 1 is displayed, 0 is
> hidden, 2 is conditional on atom display.
> 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 Jun 23, 2016, at 9:44 AM, Nicholas Hyman <
> nicholas.j.hyman at vanderbilt.edu> wrote:
> >
> > Hello,
> >
> > I have been working with labeling EPR restraints on a protein model
> through chimera. I would like to show a label of the distance between two
> residues and color it to show how well the model fulfills the restraint.
> >
> > I worked with the distance function, but I could not figure out how to
> change the color of the label through the command line, as there are quite
> a few restraints. I was able to achieve the desired result by writing a
> python script that makes a pseudo bond file.
> >
> > My issue is that in order for the labels to be shown, atoms must also be
> displayed. This creates a lot of complexity and makes the labels difficult
> to read. I was wondering if there is any way to keep only the ribbon
> display but add the labels in still? Please let me know what you think.
> >
> > Thanks,
> > Nicholas Hyman
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