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
>>
>> ------------------------------------------------------------------------------
>> Go from Idea to Many App Stores Faster with Intel(R) XDK
>> Give your users amazing mobile app experiences with Intel(R) XDK.
>> Use one codebase in this all-in-one HTML5 development environment.
>> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
>> OSs.
>> http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
>> _______________________________________________
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
--
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
------------------------------------------------------------------------------
Go from Idea to Many App Stores Faster with Intel(R) XDK
Give your users amazing mobile app experiences with Intel(R) XDK.
Use one codebase in this all-in-one HTML5 development environment.
Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs.
http://pubads.g.doubleclick.net/gampad/clk?id=254741911&iu=/4140
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
