VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 23 2003 - 15:30:28 CDT

Paul,
  For the PDB loading part of your problem, I have a solution though its
not the ideal solution:
  - VMD cannot presently load a multi-structure PDB and populate the
    "beta" or "user" fields with time varying data, though we are working
    out how to support this.

  - VMD can be forced to create a short text file containing the
    time varying "beta" values by loading a bunch of individual
    PDB files one at at time, processing them and deleting them.
    Once this external file of beta values is created, you can load it
    into VMD with a script similar to the small fragment I emailed a
    few minutes ago, setting the "user" values for each atom by reading
    them back from this file we created previously. The only trick in
    this process is that you'd need to split that big multi-structure
    PDB file into a bunch of individual files first, since we haven't
    yet taught VMD to save anything other than coordinates from such
    PDB files. (We'll probably have to change our plugin API to make
    that possible..) In the mean time, this script based mechanism is
    a way to get the job done.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 22, 2003 at 06:44:35PM -0700, Paul Tangney wrote:
> Dear VMD-l,
>
> I have tried the new beta version of VMD.
> I have a long PDB trajectory from which I would like to color the atoms
> according to "beta" and I would like to update this coloring at each step.
>
> Apparently this is implemented in the new version but I can't seem to get it
> to work. Selecting "Update color every frame" under "Graphical
> Representations"
> doesn't seem to make any difference.
> Can anybody help me with this ?
>
> Thanks in advance,
>
> Paul 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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