Dear Ioannis, You can change the VDW radius of the ion with the "atomRadius" option of the "size" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html> The default initial display of the ion is sphere style, at full VDW radius. Ball scale has no effect because it is not in the ball style. Default initial display is explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/autostyle.html> Besides the command, you can use the GUI to change VDW radius, e.g. select the ion with Ctrl-click, then click the green magnifying-glass icon (far right in the toolbar "Home" tab) to open the Selection Inspector. In that dialog, Inspect "Atoms" ... there will be various settings such as Radius that you can change. You can type a new value and press return to apply it. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html> Another way to open the Selection Inspector is with the menu: Actions... Inspect 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 Jun 13, 2024, at 7:49 AM, Ioannis Skalidis via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear all,

I want to show a metal ion surrounded by some side-chains for a figure panel, but the ion ball representation is quite small and gets lost in the figure panel. Is there a way to select only the specific ion and increase its size? I tried a bit with the "size" command, including the ballScale option but I had no luck. Any suggestions?

Thanks a lot, Ioannis.