From: John Stone (
Date: Wed Apr 30 2014 - 22:07:48 CDT

I didn't see an attachment to your email, but the answer is that
the water boxes have usually been rendered using the QuickSurf
representation (recent versions of VMD) or MSMS (older versions).
QuickSurf is a particularly good choice for this because it handles
large structures well and it allows for easy tuning of surface detail.
Try it out and let us know if you have specific questions.
You will want to choose a good transparent material. I'm particularly
fond of the "GlassBubble" material, using the VMD GLSL rendering mode,
and/or Tachyon ray tracing.

  John Stone

On Thu, May 01, 2014 at 01:46:31AM +0000, de Waal, Parker wrote:
> Hi Everyone,
> I've seen a number of VMD generated figures showing a beautiful (surface?) water layer, see attachment, and have been unable to replicate this myself.
> If anyone could offer insight into how to make such a visualization I would be greatly appreciate it.
> Best,
> Parker

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