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

[Andrew K. <ajk...@gm...>]

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...@um...