Hi Florian,
I think it is pretty convincing that refinement went all right and
the mean B you get is what it actually is. Also I just looked at
the files that you sent me the other day and I did not notice
anything suspicious.
Pavel
P.S.: Sorry if you received multiple copies of this email: I was
trying to attach a tiny image with some PDB statistics but our
server did not let me do it.
On 3/21/13 1:00 AM, Florian Brückner wrote:
Dear Pavel
yes, the refinement did converge. I did 6 macrocycles and in
separate runs started from different average atomic B-factors of
32, 66 and 97 keeping the distribution as in the original high
resolution molecular replacement model from the same crystal
form (i.e. adding 0, 34 and 65 to all atomic B-factors in the
starting pdb). In all cases after 6 macrocycles I get an almost
identical distribution of B-factors and also average B-factor of
about 52. Also setting all B-factors to the same value of 66
gave a similar distribution after refinement with an average of
52. However, in the latter case the R-free was about 2% higher
compared to starting from the original distribution, but it
dropped by about 1% during refinement.
Best regards
Florian
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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-------------------------------------------------------------
Dr.
Florian Brückner
Laboratory of Biomolecular
Research (LBR)
OFLG/102
Paul Scherrer Institut
CH-5232 Villigen PSI
Switzerland
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