VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 09 2010 - 10:39:57 CST

Thomas,
  The issue is that in VMD, the "beta" field is not stored independently
for each timestep, but rather once per molecule. You can load the beta
field into one of the "user" per-atom-per-timestep fields however to do
what you have in mind. I believe this is discussed in one of the VMD
tutorials (maybe Axel's CPMD/VMD tutorial if I remember right?)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 09, 2010 at 05:26:16PM +0100, Thomas Steinbrecher wrote:
> Dear vmd users,
>
> I am puzzled what I am doing wrong here:
>
> I have a trajectory (one file of multiple pdb snapshots of the same
> molecule separated by END cards) along which a property of my molecule
> changes. The value of that property for each atom is written in the
> beta column of the pdbs.
>
> When I load the file, it recognizes the number of frames and when I set
> the color representation to 'beta', the first frame is colored
> correctly. However, when I view the trajectory, the colors dont change,
> even if I set 'update color every frame' in the trajectory tab (yes,
> the actual numbers in the pdb do change).
>
> Is there something obvious I am missing? Im using vmd 1.8.6 btw.
>
> Kind regards,
>
> Thomas
>
> Dr Thomas Steinbrecher
> Universität Karlsruhe
> Inst. f. phys. Chemie Abt Theor. Chem. Biol.
> Vincenz-Prießnitz-Str. 1
> 76131 Karlsruhe, Germany
> phone ++49 721 608 5703
> fax ++49 721 608 5710
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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