It look like PyMOL uses atomic VdW values to draw spheres even for species that are better suited with ionic ones, like metal ions in solution.

A very old wiki page says they're harcoded, and putting a command like

    alter (name Mg), vdw=0.72

in pymolrc is ineffective, since it's executed before loading any atoms.

Is there any way to substitute in proper values automatically?



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