eleanorOh dear - why don’t crystals behave better!
Re twinning - do the data processing Plots indicate twinning? ( L
test?2nd moments?)
It sounds rather more like overlapping diffraction where only some of
the observations are Affected.
Eleanor
On Thu, 21 Jul 2022 at 10:50, Flaig, Ralf (DLSLtd,RAL,LSCI)
<00008308ad6ea74c-dmarc-requ...@jiscmail.ac.uk
<mailto:00008308ad6ea74c-dmarc-requ...@jiscmail.ac.uk>> wrote:
This paper by Pietro Roversi might help:
https://journals.iucr.org/d/issues/2012/04/00/ba5182/index.html
<https://journals.iucr.org/d/issues/2012/04/00/ba5182/index.html>
Kind regards,
Ralf
-----Original Message-----
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Kay Diederichs
Sent: 20 July 2022 22:11
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] symmetry possibilities
Dear Jorge,
what you write makes sense to me, and I cannot answer your
questions. This is just to say that the situation you encounter is
not completely uncommon, although most crystallographers would
abandon such a crystal form, I guess.
The technical term that describes this 4-fold twinning is
"tetartohedral twinning" (in contrast to merohedral twinning,
which involves two twin domains); maybe this helps to find
additional pointers.
best wishes,
Kay
On Wed, 20 Jul 2022 11:10:04 -0300, Jorge Iulek <jiu...@gmail.com
<mailto:jiu...@gmail.com>> wrote:
>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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