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Hi, we're trying to figure out how close two subunits of a protein are
to each other. We've done select <residuesXYZ> around 6 and got one
residue from the other subunit, but then when we reverse the process
using the found residue we don't pick up anything on the first subunit.
I did a bit of experimenting to see exactly what was being picked up,
and it turned out the first select was catching just one atom of the
residue in the other subunit. So then I did select <that atom> around
6 but still didn't pick up anything on the first subunit. Does that
make sense? I know what I mean anyhow. So what exactly is pymol
measuring when it does a <select ... around> thing?
University of Otago
Tel 64 3 479 7704
I try to select the atoms surround a PHE ring and I use the 'around'
expression. With a value of 4 selects almost the whole molecule and
with a value of 1 selects considerably less atoms but with a random
distribution through the molecule. What actually I'm looking for is to
represent the surface surrounds this ring like in all the ligand
examples in many tutorials.
Might be something wrong with the selection or with the syntax????