From: Anton Arkhipov (
Date: Thu Sep 25 2008 - 11:29:20 CDT


I just wanted to add that the water box actually can be also drawn
using MSMS, using a transparent material.

If you want, I can send you the VMD saved state that I used to prepare
that image.


On 24 Sep 2008, at 21:49, Peter Freddolino wrote:

> Hi,
> for the water box, the vmd volmap plugin with a transparent surface
> representation.
> The surface is an msms surface (actually, several overlapping
> surfaces, since msms chokes on such large structures) colored by
> position. The cross section is created by not including in any of
> the msms selections atoms within a certain angular region.
> The pipe representation is a thickened tube rep, if I recall
> correctly.
> Hope this helps.
> Peter
> Dong Xu wrote:
>> Hi
>> I'm particularly curious about how to create the cross section, the
>> water box, the surface and the pipe representation inside the
>> surface?
>> Please enlighten me.
>> -DX