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/
----
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
