Hello,
That is not a bug:

As it says in the help for the "size" command, "ballScale" always applies to the whole model. 
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html>

To change the ball size individually per atom or residue within a model, you would have to change the "atomRadius" instead.  For each atom, the final size = atomRadius X ballScale.  However, that will change the results of other calculations that use atomRadius, such as molecular surface, contacts/clashes, etc.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 25, 2024, at 3:42 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX users !
>
> I've just found a small bug in the protein-ligand representation.
>
> if I try to change the representation of ball and sticks using:
> style protein ball
> size protein ballScale 0.18
>
> it changes the ball representation for the both protein and ligand (e.g. defined as :lig in the system).
>
> While there is not problems with sticks:
> size protein stickRadius 0.12
> size :lig stickRadius 0.18
> So it can be applied selectively on the both selections
>
> Many thanks in advance for any suggestions !
>
> Enrico