VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 12 2003 - 14:32:00 CST

Tyler,
  I've been planning to expose the full capabilities of VMD's internal
rendering code to the scripting interfaces at some point, but I've been
holding out just a little while longer as I complete various long-term
structural changes. The ultimate goal is to allow users to write
rendering plugins to draw their own molecular representations etc.
Doing this, particularly versioning of the API and parameters, is quite
tricky, so I've held off until I came up with an idea of how to handle it
all. I've got a more concrete plan for how to implement the rendering
commands in a way that can be exposed to a plugin and/or scripting interface
now, so its just a matter of having time to pursue it vigorously. :)

In the short term, I could at least add a couple new "draw" commands until
we have these other things implemented. I've been planning to add a draw
command for per-vertex-colored triangle meshes, with RGB triplets per vertex
soon, when its available, I'll definitely let you know.

Thanks,
  John

On Fri, Dec 12, 2003 at 11:24:06AM -0700, Tyler Luchko wrote:
> On Fri, 12 Dec 2003, John Stone wrote:
>
> >
> > Dear Tyler,
> > Drawing individual triangles with Tcl will be many times slower than
> > the built-in MSMS interface because they will be rendered one at a time
> > independently of each other, with no connectivity information. As such,
> > they cannot be automatically optimized by ACTC. Internally, VMD does
> > have the means to draw aribtrary RGB colors for triangles, the color scale
> > used by VMD is meant to be a convenience for the Tcl interface.
> >
>
> Would it be possible to add a graphics color command that takes an
> aribtrary RGB value in a future version? Personally, I would find this
> quite useful.
>
> > What sort of surfaces are you generating that you can't create
> > using the built-in MSMS interface in VMD? What parameters are you
> > passing MSMS in your scripted version?
>
> In this case I've been painting the surface based on the electrostatic
> potential at the surface of the protein. I was hoping to keep this open
> as a general method as well. I.e. I could use any value that I calculate
> at the surface to paint the surface with in VMD.
>
> Thanks,
>
> Tyler
>
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Thu, Dec 11, 2003 at 03:37:33PM -0700, Tyler Luchko wrote:
> > > Hello,
> > >
> > > I've been trying to visualize surface properties that VMD does not
> > > natively suport by calling MSMS myself and drawing the triangles in VMD
> > > using TCL with my own colouring for the faces. The problem is that
> > > this is _extremely_ slow. It is slow to draw, slow to rotate and
> > > surprisingly slow to delete the faces. I've noticed that VMD uses ACTC
> > > Triangle Consolidation for drawing the MSMS surfaces and I was wondering
> > > if it is possible to use this from TCL as I assume that it would make
> > > things faster.
> > >
> > > Also, I was wondering, what are the chances that VMD will allow colouring
> > > with an arbitrary RGB triplet in the future? This would be much
> > > preferrable to using the 1040 colour pallet.
> > >
> > > Thank you,
> > >
> > > Tyler
> > >
> > > ________TyLer_LuchKo__::__MaSters_StuDent__->>__DePartMent_Of_PhysIcs_________
> > > _______UnIVerSiTy_Of_AlBerTa__->>__EdMonTon__->>__AlBerTa__->>__CanADa________
> > > ____http://Phys.UAlBerTa.Ca/______________________tluchko@Phys.UAlBerTa.Ca____
> > > _______________________780-492-5519__(But_SomeTimes_3552)_____________________
> >
> > --
> > 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