From: Olaf Lenz (olenz_at_icp.uni-stuttgart.de)
Date: Mon Nov 04 2013 - 01:39:53 CST

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Hi!

On 11/04/2013 02:58 AM, sunyeping wrote:
> I select an atom and show it as vdw. I change the sphere scale to
> make the sphere that represent the atom shown as vdw reach a
> certain size. Is there anyone know I to define the radius of the
> current sphere? Thanks.

Usually, the (van-der-Waals-)radius is defined by the type of the atom.
VMD uses some heuristics on the atom name and element to determine what
radius it has.
However, some file types also support to set the radius directly, for
example the VTF format:

  https://github.com/olenz/vtfplugin/wiki/VTF-format

I don't know what other formats support this.

Alternatively, you can modify the radius via the Tcl interface of VMD.
For example, the following two lines will set the radius of atom number
17 to a radius of 3.0:

set sel [atomselect top "index 17"]
$sel set radius 3.0

Olaf

- --
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607
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