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
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 molecul
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 o
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
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 solu
