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> wrote: > This paper by Pietro Roversi might help: > > 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> On Behalf Of Kay > Diederichs > Sent: 20 July 2022 22:11 > To: 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> 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 > > > >####################################################################### > ># > > > >To unsubscribe from the CCP4BB list, click the following link: > >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > >mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > >available at https://www.jiscmail.ac.uk/policyandsecurity/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. 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Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
