From: John Stone (
Date: Tue Sep 23 2014 - 21:00:29 CDT

You can use VMD atom selections based on the atom coordinates along
with "same residue as" to achieve what you're looking for. There are
many examples in the user's guide and past mailing list discussions that
will likely prove useful.

  John Stone

On Wed, Sep 24, 2014 at 01:27:08AM +0000, Parker de Waal wrote:
> Hello everyone,
> I?ve recently been working with membrane protein simulations, generated by the CHARMM-GUI membrane builder and simulated in AMBER, and am trying to figure out a way to trim down on excess system padding (resulting from the unoptimized GUI).
> What I would like to do is be able to take the generated protein/membrane PDB, select a rectangular region with origin x,y,z and dimensions a,b,c, and then delete everything else that doesn?t fall within that selection. This way I can reduce my atom count and help get more ns/day for the simulation.
> Does anyone know if this is possible in VMD, or perhaps another tool?
> Best,
> Parker

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