VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 19 2008 - 13:25:49 CDT

Tim,
  Can you verify that you don't have overlapping representations there?
If you do, that's probably why the spheres don't match the color of
the cylinders. If not, then the next thing to check is wether you've
got the material properties set consistently.

Cheers,
  John

On Thu, Jun 19, 2008 at 07:17:27PM +0100, Tim Carpenter wrote:
> Hi John,
> Yeah the only reason i want the CPK representation too is because the coarse
> grain models im using look pretty rubbish when represented just using
> dynamic bonds (none of the other representations will trace a backbone).
> Here are two images - one snapshot, the other tachyon. they are close-ups of
> the helical region of just one frame coloured to timestep.
>
> Cheers,
>
> Tim
>
> 2008/6/19 John Stone <johns_at_ks.uiuc.edu>:
>
> >
> > Tim,
> > One more thing: if the coloring problem your having is unrelated
> > to having reps overlapping each other, send me an example image from
> > snapshot and one from Tachyon so I can see precisely what your problem is.
> >
> > John
> >
> > On Thu, Jun 19, 2008 at 01:02:04PM -0500, John Stone wrote:
> > >
> > > Hi,
> > > If you have multiple overlapping representations, you may get different
> > > results when rendering using an external renderer than when rendering
> > with
> > > OpenGL. In order to avoid this problem, either make the CPK sphere radii
> > > slightly smaller/larger for the different reps, or make sure to set
> > > appropriate atom selections so your reps don't overlap each other.
> > >
> > > Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Thu, Jun 19, 2008 at 06:48:40PM +0100, Tim Carpenter wrote:
> > > > I have been rendering some clusters of Coarse Grain proteins using
> > Tachyon.
> > > > I have displayed multiple frames (10) and have coloured them according
> > to
> > > > timestep. To get a reasonable backbone trace i have used dynamics
> > bonds, and
> > > > also CPK representations on the CA-particles. On the screen these
> > appear to
> > > > be the same colour, however when this is rendered using Tachyon, or
> > > > TachyonInternal the CPK spheres adopt a different colour. This also
> > occurs
> > > > when using VDW spheres or beads. It also occurs when using the CPK
> > spheres
> > > > on their own.
> > > > Any ideas?
> > >
> > > --
> > > 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/ <http://www.ks.uiuc.edu/%7Ejohns/> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > 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