Dear Ivan,
well, with diffraction anisotropy you don't really have a choice, and it
would be too bad to not include all those good higher resolution
reflections.
Diffraction anisotropy follows an ellipsoid, and staraniso gives you the
ellipsoid completeness, which I think is a very useful number. This way
you know if you have collected all the data for your crystal. For my
last one, I had more then 70% ellipsoid completeness in the high
resolution shell, compared to only 11% spherical completeness...
You can also compare your anisotropy to the PDB in Robert et al., SciRep
2017.
the question of "where to cut the data" is in my opinion best answered
by the electron density map. After some resolution, including a few %
completeness will not get you better maps, but rather enhance the noise.
About Table 1, there is no consensus at the moment. I find it best to
report all that you have, prior and after anisotropic correction (if you
do so), and the refinement that goes with it. It is not a standard case.
If you use staraniso, BUSTER is a safe refinement software to go to
afterwards.
I'll let others comment on reflection filling.
Best regards
Vincent
Le 02/08/2019 à 04:10, Ivan Shabalin a écrit :
Dear CCP4BB,
There seems to be a general consensus for extending data to higher
resolution to include as much meaningful data as possible.
"Meaningful" can be defined in different ways. I heard/read opinions
such as 0.5 CC1/2, 0.3 CC1/2, 0.15 CC1/2, and stepped (paired)
refinement. The latter seems to be one of the most rigorous options
according to many crystallographers.
Including more data sounds like a good thing, but, it sometimes
results in low completeness in high resolution shells. As far as i
understand, this may result from:
a) anisotropic diffraction (if a software cuts of resolution in
non-isotropic way)
b) sub-optimal data collection (e.g. due to limitations of the
instrument, such as minimum detector distance allowed, absence of
kappa, limits on oscillation range)
In the commonly referred paper, the completeness is 96% in the highest
shell (Karplus, P. A., & Diederichs, K. (2012). Linking
crystallographic model and data quality. Science (New York, N.Y.),
336(6084), 1030–1033.) In other words, these tests were performed for
an almost complete dataset.
I used to think that more data is always better, but, as I learned
recently from Clemens Vonrhein, the resulting low completeness may
cause model bias in the maps.
Indeed, REFMAC by default tries to restore missing reflections, which
are approximated as DFc
(https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html).
We tried using the keyword "mapcalculate free include" and
"mapcalculate free exclude" for one of our structures (~1.3A, P1), and
it did seem to improve the maps a little - we saw more meaningful
features.
But, I still have several questions:
1) Does using "mapcalculate free include" in REFMAC represent a sound
solution to this problem? Does this "no fill-in at all" solution
constitute a significant problem?
2) Are there any other concerns about using data with low completeness
in highest shells?
3) STARANISO website suggests a way of handling this problem
(http://staraniso.globalphasing.org/test_set_flags_about.html). But,
would not REFMAC "fill-in" all the reflections for map coefficients
calculation to isotropic completeness anyway?
4) What is your personal approach to handling this issue? Is there
completeness value in the last shell that is too low to include it in
Table 1?
Many thanks,
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/
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Vincent Chaptal, PhD
MMSB -UMR5086
Drug Resistance and Membrane Proteins Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
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