Andrew,
The 'byres' selector expands the inner selection to include all covalently
bonded atoms. Thus, your selection #2 should be a superset of selection #1.
Are you sure that's not the case?
What do your 'wats' and 'solute' selections refer to? Are you trying to
find the water molecules to some selected organic solvent molecule? If so,
you might mean
select wats within 3 of (bymolecule solute)
This would first expand selection 'solute' to encompass any covalently
connected atoms, then would return any atoms from selection 'wats' which
are within 3Å of the resulting molecule.
A more complete explanation of what you're trying to select (and which PDB
entry, if applicable) would be helpful.
-Spencer
P.S. You might also be interested in the predefined keywords 'solvent' (all
waters) and 'organic' (ligands, buffers).
On Wed, Dec 2, 2015 at 3:32 PM Andrew Kalenkiewicz <ajkalenkiew...@gmail.com>
wrote:
> Dear PyMOL users,
>
> I'm wondering if anyone knows how exactly a selection is defined if you
> utilize both the "bymol" and "within" commands together. For instance,
> consider the following two selections:
>
> 1. "select closewats, wats within 3 of solute"
> 2. "select closewats, bymol (wats within 3 of solute)"
>
> In the latter case, it seems to me that the distance cutoff imposed by
> within is not by "closest atom" for each respective molecule (which is what
> I actually want). Visually, I can see that the first selection includes
> more total water molecules than the second selection. So what does the
> distance cutoff refer to? The geometrical center? Center of mass? I
> couldn't find anything on the PyMOL wiki that explains this.
>
> Thanks,
> Andrew
>
> --
> Andrew Kalenkiewicz
> Biomedical Engineering M.S.E. '15
> Cellular & Molecular Biology B.S. '13
> University of Michigan, Ann Arbor
> 734-709-0355
> aj...@umich.edu
>
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