From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Feb 02 2007 - 13:36:13 CST

On Fri, 2 Feb 2007, Veronika Brazdova wrote:

VB> Dear Axel,

dear veronika,

VB> Thanks for the explanation. I have several pdb files with coordinates,
VB> no trajectories. I am trying to build models of different sizes by adding
VB> chunks of protein and some waters together.
VB>
VB> I thought I'd simply take the whole protein and do a selection, but
VB> then I was using "water within 2 of something" and it would just select
VB> the atoms that were within 2 A of something, not the whole water molecule
VB> which has at least one atom within 2 A... So now I to write the atoms to

you have to realize that computer programs have no idea of your
intentions are, but do exactly what you are asking for (anything
that matches the 'water' macro and is within 2\AA of something).
what you want to use is an additional restriction to select only
whole residues. so: 'same residue as (water within 2.0 of <something>)'
should do what you want.

special reminder: this is one of the examples, where the difference
between residue and resid can be significant. residue is guaranteed
to be unique; resid is whatever number you read from the pdb file.
many MD codes re-use the same residue ids for different chains or
parts of the molecule.

VB> separate (small) pdb files and edit them by hand (adding all atoms for
VB> each molecule) and then I'd like to put them together. (Not by hand,
VB> preferably, because I'd have to renumber all atoms.)

ouch. note the above is a frequent problem and has been
commented on several times on the VMD list.

cheers,
   axel.

VB>
VB> Any thoughts on this procedure would be also greatly appreciated.
VB>
VB> Thanks
VB>
VB> Veronika
VB>

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
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