VMD-L Mailing List

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Thu Sep 25 2008 - 11:29:20 CDT

Hi,

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.

Anton.

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
>>
>> 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
>>