Andrew,
Can you provide an example? In my tests the bymol and within operators work
as expected.
fetch 4FC1 #high-res neutron scattering structure with water hydrogens
select solvent w. 3 of resi 7
stored.i=0; cmd.iterate("sele", "stored.i+=1"); print stored.i #7 atoms
select bymol solvent w. 3 of resi 7
stored.i=0; cmd.iterate("sele", "stored.i+=1"); print stored.i #12 atoms
Is this an MD structure? It's a bit weird that you have hydrogens on your
waters. Some MD programs I've worked with give poorly constructed PDB
files, so I wonder if it could be a problem with your input structure.
-Spencer
On Wed, Dec 2, 2015 at 8:58 PM Andrew Kalenkiewicz <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>
> 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> 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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>>
>>
>
>
> --
> 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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