[chimerax-users] labelling hbond atoms

[Elaine Meng]

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 at 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