Dear Amith, The "hbondatoms" specifier only works for the default h-bond model name, "hydrogen bonds": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin> Instead you can use "select true" and then label the selected atoms, e.g.: hbonds (#1.1 & protein) restrict (#1.2.* ) distslop .2 reveal t rad .2 color gold name HBONDS-1 select true la sel residues font "Rockwell Extra Bold" height .6 bg 20,20,20 hbonds(#1.1 & ~protein) restrict(#1.2.*) distslop .2 reveal t rad .2 color magenta name HBONDS-2 select true la sel residues font "Rockwell Extra Bold" height .6 bg 20,20,20 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html> A few other things about your hbonds commands: (1) you could just use #1.2 instead of #1.2.* -- the first one specifies everything under #1.2 (2) my tests suggest you also need to add the "interSubmodel true" option to your commands find any hbonds. However, this may be be due to my test only having a #1.2 model, not sub-submodels of #1.2. I also see that "hbonds delete HBONDS-1" does not work even though the model name is indeed HBONDS-1 as shown in the Model Panel. This may be a bug, but you can still close the model just using the Model Panel or the "close" command. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 13, 2021, at 8:52 PM, Rangarajan, Amith via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Group, I have a possibly rookie level question. When i use name flag with hbonds command to define two groups of hbonds like this

hbonds (#1.1 & protein) restrict (#1.2.* ) distslop .2 reveal t rad .2 color gold name HBONDS-1

hbonds(#1.1 & ~protein) restrict(#1.2.*) distslop .2 reveal t rad .2 color magenta name HBONDS-2

then when i try to label the hbond atoms ,

la hbondatoms residues font "Rockwell Extra Bold" height .6 bg 20,20,20

I am not getting the labels. I am not getting any errors so i figured that it got to do with hbonds being given a name , however i am not able to fix this. welcome to hear your suggestions. thanks again., amith