Re: [Jmol-users] closed surfaces in a cluster

[John K. <jwk...@al...>]

Three great answers! Thank you gentlemen.


On Thu, Jun 12, 2025 at 1:16 PM Norwid Behrnd via Jmol-users <
jmo...@li...> wrote:

> On Thu, 12 Jun 2025 11:10:57 -0800
> John Keller via Jmol-users <jmo...@li...> wrote:
>
> > Is it possible in Jmol to create a molecular surface around just one
> water
> > in, for example, a 2-water cluster? Then, create (and display at the same
> > time) a molecular surface around the other water molecule?
>
> One approach could be the selection of the atoms of interest by their index
> (which starts by 1) which Jmol manages by the variable of `atomno`.  Let's
> assume the .mol block you shared is saved as file `2water.mol`, a minimal
> example to develop further can be
>
> ```
> load 2water.mol;
> select atomno<4;
> geosurface vanderwaals 80%;
> write "example.png";
> ```
>
> As you see pivoting the model, the two molecules are this close to each
> other
> that the two van der Waals surfaces would overlap with each other.  Thus --
> despite scaling to 80% of the radii implemented -- the single surface
> depicted
> (cf. attached .png) still is somewhat "open" (the  critical threshold to
> close
> this one is about 72%).
>
> Best regards,
>
> Norwid Behrnd
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