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
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