Thanks Kay and Ralf for your input.
I will check out the reference pointed and search for more.
Best wishes,
Jorge
-------- Forwarded Message --------
Subject: symmetry possibilities
Date: Wed, 20 Jul 2022 11:10:04 -0300
From: Jorge Iulek <jiu...@gmail.com>
To: CCP4BB@JISCMAIL.AC.UK
Dear all,
We had some data collections at a Synchrotron. Crystals are a kind
of brush like (lattice strains, to use a term by Dr. Bergfors, though we
employed good effort for purification), but we took advantage of the
Synchrotron microfocus.
Some of the datasets (images) clearly shows more than one lattice
(maybe more than two) that, struggling, we managed to process a get a
dataset which allowed molecular replacement and then (initial) refinement.
But, in a second Synchrotron travel (and after efforts for
improving crystals), we got in some cases images with spots "well
separated' "unique lattice" at some of the target spots (radiation on
the crystal) in the crystal.
We processed these happily to P212121 (though some strange points
by pointless and/or xtriage, namely that " the L-test suggests that the
data may be twinned, so the indicated Laue symmetry may be too high").
Systematic absences seem to be OK for lower resolution reflections, but
at higher resolution there seems to be more of a modulation (if a look
at a P222 processing).
Anyway, we took, initially, refinement at P212121, nevertheless (I
should say not surprisingly), it stuck at 30/31 % R-free, model close
(if not at all) to completion. Data resolution is 2.31 A.
We went to process these images in P1, and in the three possible
P21 (named P21_45, P21_122 and P21_155 - according to approx. axis
dimensions) sg's. Then we went to refine (refmac, twin option) the
current model (and then due "symmetry copies" produced with pdbset and
added to the model to be refined,) in all possible space groups, and
*care was taken* to inherit the former r-free set *and* make the then
corresponding twin related reflections to be in the r-free set (to be
close to 5% of reflections, but "independent" reflections). It turned
out that the R/Rfree values dropped around to ~19/25% for P1 and one
(namely, P21_b151) of the P21; higher values for other P21's. As
expected, twin domains refine more or less close to 25 (P1) and 50% (any
P21), respectively.
To mess up a bit more, I made the same study with "another dataset"
(another illuminated spot on the - same - crystal). In this case, only
the dataset processed in P1 presented "good" R values.
I think these observations might correlate to what the "crystal "
physically is... a mix of portions genuinely P212121 but mixed, more or
less, that in some places with twins in one or more other types,
depending on where I focus my beam.
Should I look at anything else to establish twin P1 is the best way
to refine this structure?
Related, and a question I mentioned before in this forum: what if a
genuine 2 axis (say , P222 to P2, or even to P1) (I do not mean this is
the case here) is ignored such that one would have doubled the number of
observations but also doubled the number of parameters to be refined
(suppose to exclude NCS in any case). Would one expect R/Rfree values to
be similar in both P222 and P2 (or even P1)? How much extra freedom
would one have besides the twin domain fractions to refine?
Yours,
Jorge
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