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
________________________________
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Katherine Sippel
Sent: Monday, June 04, 2012 8:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb]
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 <epozh...@umaryland.edu>
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
