VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Sep 24 2008 - 21:49:25 CDT

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
>
> http://www.newscientist.com/blog/technology/uploaded_images/0306viralcomputer_b-755960.jpg
>
> 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
>