VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 13 2010 - 10:43:47 CDT

Hi guys,
  Given the litations of the method used by QuteMol, I think just exporting
your static VMD structure to a PDB and viewing it with QuteMol would be the
best thing in the short-term. There's little reason to implement such a
limited method in VMD itself since it won't work for so many things, but
I think it makes perfect sense to use VMD to feed QuteMol if all you want is
to view a static model as a set of spheres. I'll let you all know when
there's an SSAO version of VMD to try, but it will be a while yet.

Cheers,
  John

On Wed, Oct 13, 2010 at 01:01:01PM +0200, Ajasja Ljubeti?? wrote:
> Thank you for all your replies.
> I agree with Boris, that AO would already be useful despite the given
> limitations (static structures and only spheres). It could be hackishly
> implemented as another rendering mode.
> Also I guess it would be possible to write a simple script that would
> export a selection to a PDB as well as a custom color file for use in
> QuteMol.
> Best regards,
> Ajasja
>
> On Wed, Oct 13, 2010 at 08:37, Marc Baaden <baaden_at_smplinux.de> wrote:
>
> Dear Ajasja,
>
> Although your question was about VMD, I just wanted to let you know
> that there is a software around that does real-time ambient occlusion.
> It is called Yasara [1] and has a free viewer, then additional modules
> that cost some money. I am in no way affiliated with them.
>
> I also think it is implemented in Michael Sanner's PMV software [2].
>
> As a side note, we are also working on real-time ambient occlusion,
> which right now works for static structures, and hopefully in the not
> so distant future for trajectories.
>
> Kind regards,
> Marc
>
> [1] http://www.yasara.org/
> [2] http://www.scripps.edu/~sanner/
>
> --
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden_at_smplinux.de - http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 

-- 
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