VMD-L Mailing List

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Thu Aug 27 2009 - 11:02:46 CDT

Hi, Naren:

You can try *MSMS* with this more transparent material defined as :
Ambient 0.30
Diffuse 0.50
Specular 0.87
Shininess 0.85
Opacity 0.11

Best,
Bin

On Aug 27, 2009, at 8:14 AM, 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
>