CPK and Ball&Stick

Try doing something like this in your shortcode:

[jsmol acc=<accession> commands='=spacefill only; spacefill 23%;wireframe 0.15;color cpk;']

jsmol uses the commands parameter to set a key-value pairs. Each pair is separated by |||. The key is the label for a button and the value is what the button is told to do. Here the key is blank (note the = inside the single quote), which tells JSmol2wp to not put the following commands in a button, but instead to run them when loading the structure, or when the reset button is clicked.

To get ball and stick, we combine wireframe and spacefill

spacefill only;  # turns off any other display mode; other commands would work here
spacefill 23%; # makes the balls 23% of the VdW radius.
wireframe 0.15; # makes the sticks
color cpk; # colors the atoms

Hope this works for you.

Thank you, it worked like a charm!