In my experience, occupancies and B-factors are
correlated for small molecules, e.g. waters and here I keep the occupancy at
1.00 and only refine B-factors. However, for larger ligands e.g. Cl-, Zn2+ etc.
often a shell of red difference density around the ion indicates to me that
occupancies and B-factors do not fully compensate each other. Also, as a ligand
is either present or gone, it only makes sense to refine group
occupancies, which, again in my experience (Buster) produces quite sensible
results, even at 2.2 Å. In fact, I now refine group occupancies for everything
which is not water and not covalently in full occupancy attached to the protein,
e.g. metal ions, chloride, phosphate, sulfate etc. even at resolutions lower
than 2.2 Å.
Cheers,
Herman
Hi Ed,
I've actually run that exact test in phenix as an
exercise to prove to my PI the validity of occupancy refinement. Though as a
disclaimer it was a 1.2 angstrom data set and this was an alternate
conformation situation. I ran different input occupancies without occupancy
refinement and measure the difference density peak values and average
B-factors and ended up with the same occupancy ratio that the program's
occupancy refinement spit out. Of course this might not hold true if someone
is refining the occupancy of a ligand that is partially bound without an
alternate option (i.e. total occupancy <1). I haven't tested that one
systematically yet though I suspect Pavel has probably already done this at
some point.
Cheers,
Katherine
On Mon, Jun 4, 2012 at 7:35 AM, Ed Pozharski
<[log in to unmask]> wrote:
> Is it reasonable to refine occupancy in phenix at 2.2 A
resolution?
Implementations may differ, but imgo refining
occupancy at 2.2A
resolution is not very reasonable under most
circumstances, as it will
correlate strongly with the B-factor. A
reasonable approach might be to
fix occupancy at different levels and get
a series of refined models.
Then you look at (i) B-factor behavior and
see at what occupancy it
matches the surrounding atoms and (ii)
difference density (my
unsubstantiated theory is that if you plot it
against occupancy it
should have a central flat region where B-factors
are capable of
compensating and two linear regions on extreme ends which
should allow
to extrapolate the true value.
Refmac does occupancy
refinement. It's quite fast, so you may try
randomizing the initial
value and get some idea about
convergence.
Cheers,
Ed.
--
Oh, suddenly throwing a giraffe into a
volcano to make water is crazy?
Julian, King of
Lemurs
