VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Mar 06 2011 - 15:44:09 CST

Dow, (and other interested parties)
  I forgot to include a link to the various WebGL browsers
that are available:
  http://www.khronos.org/webgl/wiki/Getting_a_WebGL_Implementation

Here is a page that will determine if your web browser has a
working VRML and/or X3D plugin (for those that don't have WebGL),
and download links for obtaining them:
  http://cic.nist.gov/vrml/vbdetect.html

There are also standalone programs out there that will directly
display X3D files, if you want to do it outside a web browser:
  http://www.web3d.org/x3d/content/help.html

Cheers,
  John

On Sun, Mar 06, 2011 at 03:28:46PM -0600, John Stone wrote:
>
> 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 

-- 
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