[Chimera-users] Displaying Labels without displaying Atoms

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 23 15:54:06 PDT 2016

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).


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 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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