VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 19 2008 - 13:54:40 CDT

Tim,
  Send me (not all of VMD-L) a tar file with a PDB/PSF for the frame
in question, along with a VMD saved state file and the Tachyon .dat file
and I'll see what's going on.

Cheers,
  John Stone

On Thu, Jun 19, 2008 at 07:52:30PM +0100, Tim Carpenter wrote:
> 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
> > 

-- 
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