From: Axel Kohlmeyer (
Date: Sat Aug 05 2006 - 12:05:51 CDT

On 8/5/06, Shatadal Ghosh <> wrote:
> Hi,
> My problem is that I want to choose a subset of atoms based on a
> particular criterion. The criterion is whether the atom contains a
> particular value in a column in the pdb file. This column is appended to
> the pdb file at columns beyond the pdb specification so the pdb file can
> be visualised in vmd.

> Can I refer to the column number in a Tcl/Tk script? I am a Tcl/Tk
> newbie and I looked through the Tcl/Tk help but was unable to find a way
> to do it.

no. since this value is in a non-standard field, it will be completely ignored
by VMD. your best bet will be to first process the pdb file externally to
create a file, that only contains the data you want to use in the selection
string and then store it in the 'user' field. see. e.g.
for an example on how to store a propery in the user field and
for an example on how to read information from an external file.

with the data in the user field you can then have selections like: user = 1 or
user < 0 and so on.

> Basically how do I write the following (which is awk-like) in the Tk
> console?
> if ($<col number> == <some value>) >> atom_selection_1

VMD does not work like this.

> I went through the selection choices in the selections tab of the
> Graphical Representations window and there are some volindex, vol and
> interpvol keywords. Can these be used?



> Thanks.
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Axel Kohlmeyer
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.