if the new data is of high enough resolution and the original
structure was solved by MR - it may be little extra (human) effort to
just redo the MR followed by automatic building.
This can have the advantage that, after building, comparing the two
structures, you may discover small mistakes in the original structure
that otherwise you would perhaps not have noticed.
Mark
Quoting Dirk Kostrewa <kostr...@genzentrum.lmu.de>:
Hi Mike and other interested colleagues,
I agree - it is best to select the observed data with the same indices
for the new Rfree set as in the previous isomorphous crystal(s),
selecting new ones for higher resolution shells (which can be
conveniently done in XDS during conversion to other formats with
XDSCONV). However, in my experience, even if a completely new random
Rfree set is chosen, it will "de-couple" from its initial bias after
many cycles of refinement, even without any random perturbations of
the model or simulated annealing. You can see how many cycles are
needed by monitoring the difference between R and Rfree, which should
converge at a maximum value if you don't change the model or the
refinement parameters in between.
Best regards,
Dirk.
Am 24.09.2009 um 10:36 schrieb Eleanor Dodson:
Mike England wrote:
Hi all,
I will appreciate your comments on the following case:
I have two datasets from the same or identical crystals. Initially, I
refine a structure against the first data set and later on switch to
another dataset for further refinements.
Do you think, my Rfree will be biased as Rfree reflections in second
dataset may be in fact Rwork reflections in previous datasets ?
Thanks in advance,
Mike
Yes [- it will be biased, but why arent preserving the same Rfree
set from crystal 1 into the crystal 2 assignmenmt, only selecting
new free reflections at the higher resolution data from crystal 2
If you are running scala or import scaled data t make an mtz file
there is an option:
Click Ensure Free R and Copy freeR from another mtz
Eleanor
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Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
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