Re: [PyMOL] using "bymol" in combination with "within"

Sampson, Jared M. Thu, 03 Dec 2015 08:22:15 -0800

Hi Andrew -

If you're just looking to expand the selection from atoms in water molecules to 
entire water molecules, I would actually use `byres` instead of `bymol`.  The 
`bymolecule` selector is apparently dependent on how PyMOL sees the bonds (e.g. 
try `fetch 3ghe, async=0; select test, bymol chain H and resi 30` -- you only 
select up to the gap at resi 127).  `Byres` should get the entire HOH residue 
as defined by the residue name and number, as long as they are unique for each 
of your water molecules.

So, in short, this should work:

select closewats, byres (wats within 3 of solute)

Or as Spencer mentioned, using the built-in keywords:

select closewats, byres (solvent within 3 of organic)

Or, if you have multiple organic components and only one of them is your
ligand, which has the residue name DRG:

select closewats, byres (solvent within 3 of resn DRG)

Hope that helps.

Cheers,
Jared

—
Jared Sampson
Graduate Student
Department of Biochemistry and Molecular Biophysics
Columbia University

On Dec 2, 2015, at 2:57 PM, Andrew Kalenkiewicz
<ajkalenkiew...@gmail.com<mailto:ajkalenkiew...@gmail.com>> wrote:

Hi Spencer,

Thanks for your response! I was also originally under the impression that my
selection #2 should be a superset of selection #1, but that is definitely not
the case. There are atoms in selection #1 that are not included in selection #2.

What I want to do is select all the water molecules that have at least one of
their atoms within 3 angstroms of my protein-ligand complex (the solute). Based
on the above discrepancy, I know that selection #2 does not give me this. This
is corroborated by an independent calculation I did in a different program (the
Bio3D pacakge in R).

All best,
Andrew

On Wed, Dec 2, 2015 at 10:53 AM, Spencer Bliven
<spencer.bli...@gmail.com<mailto:spencer.bli...@gmail.com>> wrote:
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<mailto: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<tel:734-709-0355>
aj...@umich.edu<mailto:aj...@umich.edu>
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Re: [PyMOL] using "bymol" in combination with "within"

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