From: Tim Carpenter (timcarpenter83_at_googlemail.com)
Date: Thu Jun 19 2008 - 13:52:30 CDT

Hi John,
Yup - this is just one frame from a simulation. I wanted to overlap multiple
frames to show the variation in a specific region, but just selected this
one frame as it illustrated the point quite well. I have also checked the
materials, and even tried different materials... Even if i *just* have the
CPK/VDW spheres selected they are rendered very different colours...

2008/6/19 John Stone <johns_at_ks.uiuc.edu>:

>
> 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
>