VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 21 2004 - 14:17:38 CDT

Emmanuel,
  There isn't any simple way to load the beta field of PDBs into
VMD as a time-varying field. The best suggestion I have for this
would be to write a VMD script to load each of the PDB files sequentially,
concatenating their beta fields to a single text file. Once finished, you'll
have a text file containing all of the beta values for all of the frames.
>From there, you could read the PDB files as a trajectory, and then load
the saved beta values into the "User" per-frame data field. The major
complication with your need is that your original data is in the form of
a multi-frame concatenated PDB which makes it difficult to retrieve the
beta field from individual frames. You may have to split them into
separate files with a perl script or something in order to get this done.
Sorry I don't have any better suggestion at this time. Clearly there's
a need to make VMD start storing more data fields as time-varying data
by default, but it'll have to come in a future version.

  John Stone
  vmd_at_ks.uiuc.edu

On Sat, May 29, 2004 at 09:05:16PM +0200, emmanuel.levy1_at_free.fr wrote:
> Hello,
>
> I've got a PDB with multiple structures. Coordinates are the same
> for all the structures and only the "beta" field changes. I would like
> to animate these structures to see the "beta" field evolution.
> I understood that VMD loads the beta information only from the
> first frame.
> I noticed 2 potential solutions in the mailing list but there are
> no detailed explainations about how to put it in practice:
> (i) loop over molecules instead of frame --> I coudn't manage to do it.
> (ii) it has been said that it might be possible with VMD 1.8.1 to reload the
> "beta" field in the different frame and if it is indeed, I couldn't find how.
> Many thanks to anybody who could help me !
> Cheers,
> Emmanuel 

-- 
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