VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 04 2004 - 10:54:22 CST

Sanjeev,
  It _doesn't_ load as a single PDB, but if you re-read some of the
previous responses to your original email, there are ways to visualize
it as if it were. You can use the "draw multiple frames" feature in
VMD 1.8.2 to display all of the frames simultaneously, so even though
VMD loads it as a trajectory, that's a quick-and-dirty way of seeing
the whole virus. If you really want them loaded as a single structure,
I have a script that uses psfgen to merge multiframe structures like
these into a single structure. The PDB posts these as multiframe PDBs
because they can't make a legal PDB file of the full virus otherwise,
since there are far more than 99,999 atoms. If you decide you really
want to merge them into a single structure via psfgen, you'll need
quite a bit of memory however. (around 2GB of memory as I recall..)
(the psfgen script adds the missing hydrogens too..)

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 04, 2004 at 11:41:31AM +0530, Sanjeev B.S. wrote:
> I downloaded that pdb file to my local machine and gunzipped it first
> however, how did you try to load it into VMD?
> +++ Downloaded 1sva.pdb1.gz, renamed as 1sva.pdb.gz, unzipped and then
> vmd 1sva.pdb. It loaded as an animation (60 frames) on v1.8.2. I am not
> sure why it loads as a single PDB in your case.
>
> This reminds me of another problem that I face... I have superimposed a
> set of PDBs and wanted to view them. Despite a TER card between them
> bonds were seen between different molecues. Is there a way by which this
> could be done, that is to get bonds between the appropriate molecules
> only? 

-- 
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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