Hi Shubham, If you don't mind actually deleting the distance labels instead of hiding them, you could use this instead: label delete pseudobonds That will keep the pseudobonds shown, but delete their (distance) labels. Maybe there should be an option in "distance style" to hide these labels. In your case, what you really wanted was not a distance measurement anyway (if I understood correctly). Another way to add a pseudobond is to read in a pseudobond file, which essentially lists pairs of atoms between which to draw the pseudobonds... however, making a separate file is often inconvenient. <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles> Maybe there should also be a command for making a generic pseudobond. Another kludgy way besides using the "distance" command is to force the "contacts" command to identify the two atoms/centroids as a contact by using a huge contact distance. i.e. instead of: distance [specification of two atoms] would be something like: contacts [specify one atom] restrict [specify other atom] distance 5000 make true color gold see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.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 May 14, 2022, at 11:57 PM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I hope you are doing well. I have a python script, to be executed in nogui mode, which does the following: -open a pdb file -define centroids for specific residues -draw pseudobonds between specific residues -> I am using the command distance for this purpose
The issue arises when I have to save the session (.cxs) when in nogui mode, I am getting this error: QGuiApplication::font(): no QGuiApplication instance and no application font set.
I believe it is because of the text labels created by the command distance. So, I included the following in my code: run(session, ‘hide #2.*’) and I can now save the session.
I noticed in the model panel that the pdb file is assigned to #1 and the pseudobond to #2. The text labels are created as a submodel of the pseudobond (so #2.1, 2.2,..), hence why the ‘hide #2.*’
Will this fix always work? Is the model assignment also dependent on the pdb file being opened?
Regards, Shubham