VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Mar 06 2011 - 15:28:46 CST

Dow,
  My link just contains a simple example structure (about 10MB download,
so you may need to be patient):
  http://www.ks.uiuc.edu/~johns/files/x3dom/vmdscene.html

Give it a spin and let me know if it works for you or not.

That said, once this type of example works on a good range
of browsers, one can do a lot more with adding programmatic
button controls, to turn rep styles on/off, pick things, etc.
The sorts of things are about half-way towards what can be done
in a full-fledged program, but all within a web browser,
and without needing a plugin.

Cheers,
  John

On Sun, Mar 06, 2011 at 02:55:02PM -0500, Dow Hurst wrote:
> John,
> I would like to try out the web link, if you don't mind.A I'm mainly
> wanting to be able to look at gpcr crystal structures or our in house
> models of gpcrs while mobile.A On my iTouch I could use the molecules
> program.A There didn't seem to be any equivalent for android.A The
> protein data bank has plans for an android client in the next year to
> complement their iPhone/ipad app.A There is a new app for the apple
> devices called cmol, at cmol.org.uk, that looks very interesting.A
> However, if I can use either the Dolphin browser or Firefox to view
> structures as you describe then that would suffice for now.A Taking
> measurements of dihedrals, distances, or bond angles would be the next
> step.A I did just find an older flash based viewer on tufat.com but it
> doesn't show bonds, only vdw atom displays.
> Thanks,
> Dow
>
> On Mar 6, 2011 2:39 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:
> >
> > Dow,
> > The android Java client we have been working on (slowly) is
> > meant as a way to use a smartphone as a 3-D pointer/interaction
> > device for controlling a VMD session running on a normal computer
> > (e.g. for presentations, meetings, etc).
> >
> > At the present time we don't have any serious plans to port VMD itself
> > to Android. In order to run VMD on Android (even a limited subset),
> > the GUI and the OpenGL rendering code would have to be changed to
> > fit within the limitations of OpenGL ES and a touch screen interface.
> > I would also have my doubts about the phone's battery life while running
> > a big code like VMD. :-)
> >
> > One way you could display models from VMD on a smartphone and rotate
> them
> > etc is to export the VMD scene as an X3D file (a feature of VMD 1.9) and
> > then view it using one of the WebGL-enabled browsers. One of the latest
> > beta versions of Firefox for Android is able to run WebGL, though I
> think
> > in our last test it didn't quite handle all of the javascript required
> > for X3DOM, which is a javascript X3D viewer that runs entirely
> in-browser
> > with no plugin. I expect WebGL to become much more popular in the next
> > few months as more browsers begin to support it. If you want to see an
> > example X3D object embedded in a web page, let me know and I'll send
> > you a test link to try out on your phone (requires a WebGL capable
> browser).
> >
> > Jmol is undoubtably a better route for an interactive molecule viewer
> > if the phone browsers support it.
> >
> > Cheers,
> > John
> >
> > On Sun, Mar 06, 2011 at 12:24:15PM -0500, Dow Hurst wrote:
> >> I read on the vmd-1.9 changelogs a blurb about an android Java client,
> but
> >> haven't found any other mention of this.A Is there any possibility of a
> >> 3D molecular viewer for android based on vmd?A Right now, for the
> android
> >> platform, there are no usable 3D protein or small molecule viewers. I'm
> >> looking for something that would show sidechains and ribbons for
> proteins
> >> but haven't found anything yet.
> >> Thanks,
> >> Dow
> >
> > --
> > 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