Yes - in P1 if you have two molecules approximately related by X y z. And x+ 1/2 y z say then the spots along the axis a* will have h=2n weak. And the sections with h even will have very weak spots. If you calculate a Patterson for the data there will be a strong peak st 1/2, 0,0. But you say you can find a reasonable solution in p21 21 21? Have you tried symmetry p21 with the 2fd axis along a* or c*? Also it is possible if you have multiple crystals the merging has combined crystals with similar symmetry - is your 2 fold axes- but not exact. Look at the data analysis to see if some crystals agree better than others.
On Thu, 28 May 2020 at 03:49, Ethan A Merritt <merr...@uw.edu> wrote: > On Wednesday, 27 May 2020 18:49:23 PDT Jessica Bruhn wrote: > > Hello, > > > > I am wondering if pseudosymmetry can cause weak reflections that mimic > the > > doubling of one unit cell axis' length. Has anyone seen something like > this > > before? > > Yes. > > > I am processing data from a small molecule sample collected with > electron > > diffraction from multiple crystals. For the b axis, it is not clear if > the > > length should be 10A or 20A. There are spots with the correct spacing for > > b=20A, but every other spot seems weaker than the spots along k if I > choose > > b=10A (this extends beyond (0,k,0)). I am unable to phase the b=20 data. > I > > have solved this structure in P1 with b=10 and found four molecules in > the > > ASU and in P212121 with b=10 resulting in one molecule in the ASU. > > > In P1, three of the four molecules adopt the same conformation, but the > fourth > > molecule is in an alternate conformation that causes only ~1/2 of the > > molecule to be consistent with the first three. In P212121 I see density > > for part of this alternative conformation, but the full molecule in this > > alternate conformation cannot pack properly in P212121. Based on these > > results and some orthogonal data, I think I should refine the solution in > > P1 with b=10. Does it seem reasonable that pseudosymmetry is causing > these > > weak reflections along k hinting at a doubling of the b axis? > > This description makes me think also of a supercell. This can happen > when, say, the position of one copy N is not compatible with all (N-1) of > the others positions. Some unit cells contain (N-1) copies but not the > problematic N; other cells contain the N copy but miss one or more of > the others to make room. This gives you a stochastic mix of cell > contents. If it were truly random you'd see spots for a small cell > but the contents would have to be described by partially occupied sites. > But if there is a bias towards alternation of cells +N -N +N -N you > get a pseudo-doubling of that cell edge, matching your description. > > Suggested reading: > Lovelace J, Petrícek V, Murshudov G, Borgstahl GEO. > Supercell refinement: a cautionary tale. Acta Crystallogr D Struct Biol. > 2019 Sep 1;75(Pt 9):852-860. > doi: 10.1107/S2059798319011082. Epub 2019 Aug 28. PMID: 31478908; PMCID: > PMC6719663. > > I've had to deal with these in macromolecular crystals. > I would imagine that the same can happen for electron diffraction > but I can't point to any prior examples in the literature. > > good luck! > > Ethan > > > Thanks in advance! > > > > Best, > > Jessica > > > > > > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?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/webadmin?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/
