From: Axel Kohlmeyer (
Date: Wed Mar 11 2009 - 10:15:05 CDT

On Wed, 2009-03-11 at 14:31 +0800, accomp lin wrote:

please note, that VMD by itself assumes that the number of atoms
in a system (or molecule in vmdspeak) does not change.
 the operations
you describe are done with the psfgen plugin, so please have a look
at the psfgen documentation.

as for atomselect, it is explained in the vmd user's guide
that this command generates a new "proc" with a unique name
and returns the name to it. for more details, please read the
documentation first.


> Dear developer:
> I wish to create my simulation enviroment using tcl. When I try to
> combine several PDB file into one, I'm stucked. I found a pdb merging
> script on your website , which uses a command " segment " and
> "coordpdb " to read and store several pdb together and then output
> them as one pdb using "writepdb". Can you explain how to use these two
> commands?
> Plus , what's the type of the argument dose "atomselect" command
> create?i.e. if i type ' set x [atomselect top all] ', then what is
> $x, is it a list or something? Can i add or delete atoms in $x ? If i
> can, how?
> Thanks in advance
> Jiaqi
> ______________________________________________________________________
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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.