Hi Florian,
I'm glad it works now. Regarding difference between Wilson B and
mean refined B: well, it's hard to quantify what's "too low" or
"too different". Average refined B may deviate from Wilson B and
the difference in your case does not seem to be terribly large.
Did the refinement converge? What if you do say 10 or 20
macro-cycles instead of default 3? Will B-factors further change
between macro-cycles?
Pavel
On 3/19/13 7:37 AM, Florian Brückner wrote:
Dear Keitaro and Pavel,
thank you for your suggestions. I have now used the latest
nightly build (1326). With this version, the average B-factor
converges at about 52 A**2 and also the distribution is very
similar, regardless with what B-factors I start the refinement
(I tried average B-factors between 32 and 97). So clearly the
behavior of this newest version is different from the version I
have been using before (1.8.1 stable release 1168) and also from
the latest stable release (1.8.2 stable release 1309), which
behaves the same as 1168. To me the B-factors still look a bit
too low, since the Wilson B-factor calculated by phenix is
66.45, the Wilson B-factor I determined manually from the linear
part of the Wilson plot is 97.
Best regards
Florian
Dear Florian,
Maybe you are using phenix-dev-1311 or earlier?
I am afraid that you have experienced the bug that overall
B-factor is
not applied to individual atomic B-factors in certain cases,
which I
have also experienced recently. That bug was fixed in
dev-1312 if I
recall correctly.
Hope it helps,
Keitaro
2013/3/19 Florian Brückner <[email protected]>:
Dear all
I am refining a structure at 3.2 A with phenix.refine
using automatic
optimization of target weights, solved by molecular
replacement with a 2.1A
structure of the same crystal form. Rwork=26%, Rfree=28%.
I use individual
atomic B-factor refinement. The obtained distribution of
B-factors after
refinement looks reasonable and quite similar to the
distribution in the
higher resolution model, which I suppose would be
expected, since it is the
same crystal form. However, the average B-factor does not
change
substantially, i.e. if I start with the B-factors from the
high resolution
model (average B-factor around 32 A**2) after 6
macrocycles the average
B-factor is still around 32 A**2. If I set all B-factors
to the Wilson
B-factor determined by phenix.refine (66 A**2), after 6
macrocycles the
distribution of B-factors looks again very similar to the
high resolution MR
model, but the average B-factor is still around 65 A**2.
What should I make
of this? Is this an expected behavior at this resolution,
i.e. the fact that
the absolute values of B-factors cannot be determined
during refinement,
although a reasonable distribution can be obtained as
judged by plotting
average B-factors vs. residue#? Since the average B-factor
does not change
much during refinement, which average B-factor should I
start refinement
with to end up with reasonable absolute values? I have
manually determined
the Wilson B-factor from the linear part of the Wilson
plot (4.5-3.2 A) to
be 97 A**2. This seems high to me. Would that be expected
for the given
resolution, given that the 2.1A structure of the same
crystal form has 32
A**2? I should add, that there is not a substantial effect
of the average
refined B-factor on Rfree.
Thanks for any comments or suggestions.
Best regards
Florian