VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Oct 13 2010 - 11:12:57 CDT

I found a version of QuteMol (QuteMolX) which allows some additional
options<http://www.nanoengineer-1.net/mediawiki/index.php?title=NE1_PDB_REMARK_Records_Display_Data_Format>
in the
PDB.
Now I just need to figure out how to iterate through all visible spheres in
the current scene and get their size, position and color using TCL. Any
suggestions?
Exporting just a subset to a PDB and loading it with default colors in
QuteMole is, luckily, trivial:)
Perhaps this would be best implemented as a new renderer, but I confess I
have yet to compile a custom version of VMD).

Looking forward to real-time surfaces, real-time AO rendering and multiple
pass anaglyph rendering.
(John, your todo ist is probably reeaaaallly long:)

Best regards,
Ajasja
On Wed, Oct 13, 2010 at 17:43, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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
>