Hi Timofey,
There is currently no way to automatically substitute the radii. But you can
bind a keyboard shortcut to do the substitution, maybe that's convenient enough?
Put this in your pymolrc to bind the F1 key:
python
@cmd.set_key("F1")
def update_ionic_radii(selection="all"):
cmd.alter("elem Mg & ({})".format(selection), "vdw = 0.72")
cmd.alter("elem Na & ({})".format(selection), "vdw = 0.95")
# more elements here...
cmd.rebuild()
python end
Cheers,
Thomas
> On Nov 12, 2020, at 5:50 AM, Timofey Tyugashev <[email protected]>
> wrote:
>
> 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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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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