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/
