From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 16 2004 - 15:10:06 CST

Hi,
  You can make atom selections that contain wildcard characters
as in some of these examples in the VMD User's guide:
  http://www.ks.uiuc.edu/Research/vmd/current/ug/node81.html#4979

Once you've got an atom selection that contains only the atoms you
want, you can have VMD write out a new PDB file from that atom selection
with '$sel writepdb myfile.pdb' or something similar. This is described
in the User's guide as well:
  http://www.ks.uiuc.edu/Research/vmd/current/ug/node107.html

Let us know if you need more help with this.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 16, 2004 at 11:57:51AM -0600, Streiff, John H. wrote:
> The PDB file of a protein I would like to use in a simulation has duplicate coordinates for some atoms, which are designated with an A or B before the three letter amino acid code. Is there a way in VMD to select only the A or B set of coordinates so I can prepare a pdb file of the protein without duplicate atom coordinates?

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