From: Axel Kohlmeyer (
Date: Sat Nov 24 2007 - 17:30:22 CST

On Sat, 24 Nov 2007, Francesco Pietra wrote:

FP> Once I have aligned a protein over a membrane, is any command to get
FP> rid of lipid and water residues that overlap the protein, plus a
FP> margin of say 1.5A? Better if the command is per residue, rather
FP> that per all overlapping atoms or residues.

well, did you have a look at the combine.tcl script?
you create a temporary combined file and then find the
overlapping atoms with an atom selection and delete those
atoms on a per-residue/segment basis.

FP> Also, is it any command to list overlapping residues? I want to
FP> check for any possible steric clashes.

same thing. you can use atomselect.

FP> Why am I not using the plugin combine? I was unable to get it
FP> working with my systems. However, once the cavity is created in the

you may have to make a few changes. but the script is
very simple and straightforward. please explain what does
not work. the way to do what you are asking for is exactly
how it is implemented in the script, so perhaps, you should
try building your own version by copying it over and adapting
it to your needs step by step.

FP> membrane, and I have the coordinates of the protein now fitting the
FP> cavity, I have the means to combine both, getting a usable pdb file.
FP> Thanks for your understanding toward a guy with only one foot in VMD.

well, put them both it and perhaps start by playing a little
bit with simpler examples until you "get it". it takes a bit
of patience, but once you "got it", everything will be very
simple and straightforward. trust me, i've been through this, too.


FP> francesco pietra
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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.