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
Hi!
I have a group of structures (168 in total) and I want to align all of them
to the first one in order to know the RMSD calculation. For that purpose I
use the following:
f=open('rmsd.txt','w')
rms2=cmd.align('structure_0002 and name ca','structure_0001 and name ca')
.
. (NOTE: I got all of
Hi Young-Jin,
The latest MacPyMOL works fine on El Capitan. XQuartz is not required, unless
you use the "MacPyMOLX11Hybrid" interface.
Which version do you have installed? In my tests, all MacPyMOL versions newer
than 1.4 work on El Capitan (not heavily tested, but they open and render
