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

[Norwid B. <nb...@ya...>]

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