VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 27 2009 - 10:29:08 CDT

You need to use MSMS or the volmap commands I suggested.
Surf won't work because it will create internal cavity surfaces, and
it won't perform well with very large models. The images we create
using the water boxes are all done either using the MSMS representation
or the "volmap" commands. For very large models, only the "volmap"
method is usable. To get shadows etc, we usually render these images
using the Tachyon ray tracer (see File->Render), not just using
the on-screen displayed image.
  
Let me know if you still need more help with this.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 27, 2009 at 11:14:58AM -0400, Narender Singh Maan wrote:
> Thank you John. I tried the suggestions and played around with all the
> options but somehow that effect is just not coming, especially the
> transparency and shadows. I am assuming (novice assumption) that its
> actually a VDW representation of only the outer most atoms for waterbox
> that have been merged and smoothed at the contacts.
> Anyway i have two more questions please, Is it possible to have a "smooth
> loops" function in VMD? Something like in pymols cartoon representation.
> and why is it not possible to use 'surf' on selected waterbox? When i try
> to use it, it says malloc of zero/illegal length
> Thank you again.
> Naren
>
> On Wed, Aug 26, 2009 at 2:29 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> There are some examples of this in the VMD Images and Movies tutorial:
> http://www.ks.uiuc.edu/Training/Tutorials/
>
> Basically, you can either use the "volmap" commands or the VolMap plugin
> to do this, or try the example "marshmellify" script that's included in
> that tutorial.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Wed, Aug 26, 2009 at 10:35:56AM -0400, Narender Singh Maan wrote:
> > Hello, i was wondering if anyone can guide me on how to draw
> something
> > like this
> >
> (http://www.ks.uiuc.edu/Training/Tutorials/science/membrane/mem-tutorial.pdf);
> > page 32, for water box.
> > Thank you
> > -naren
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078