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Zbyszek - do you have any measure of unintegrated streaks? It could be a help to at least have a rough score. Eleanor On 11 March 2014 20:04, Zbyszek Otwinowski <[log in to unmask]> wrote: > Shape of the diffraction spots changes in the statistical disorder <--> > > twinning continuum. At both ends spots shape is like in diffraction from > crystals without such disorder. However, in the intermediate case, > electron density autocorrelation function has additional component to > one resulting from ordered crystal. This additional component of > autocorrelation creates characteristic non-Bragg diffraction, e.g. > streaks aligned with particular unit cell axis. > > In the absence of such diffraction pattern, the ambiguity is binary. The > description of the problem indicates statistical disorder. > > Zbyszek Otwinowski > > > Hi, > > > > If there's an NCS translation, recent versions of Phaser can account for > > it and give moment tests that can detect twinning even in the presence of > > tNCS. But I agree with Eleanor that the L test is generally a good > choice > > in these cases. > > > > However, the fact that you see density suggests that your crystal might > be > > more on the statistical disorder side of the statistical disorder <--> > > twinning continuum, i.e. the crystal doesn't have mosaic blocks > > corresponding to one twin fraction that are large compared to the > > coherence length of the X-rays. So you might want to try refinement with > > the whole structure duplicated as alternate conformers. > > > > Best wishes, > > > > Randy Read > > > > ----- > > Randy J. Read > > Department of Haematology, University of Cambridge > > Cambridge Institute for Medical Research Tel: +44 1223 336500 > > Wellcome Trust/MRC Building Fax: +44 1223 336827 > > Hills Road > > E-mail: [log in to unmask] > > Cambridge CB2 0XY, U.K. > > www-structmed.cimr.cam.ac.uk > > > > On 11 Mar 2014, at 14:10, Eleanor Dodson <[log in to unmask]> > > wrote: > > > >> Sorry - hadnt finished.. > >> The twinning tests are distorted by NC translation - usually the L test > >> is safe, but the others are all suspect.. > >> > >> > >> > >> On 11 March 2014 14:09, Eleanor Dodson <[log in to unmask]> > >> wrote: > >> What is the NC translation? If there is a factor of 0.5 that makes SG > >> determination complicated.. > >> Eleanor > >> > >> > >> On 11 March 2014 14:04, Stephen Cusack <[log in to unmask]> wrote: > >> Dear All, > >> I have 2.6 A data and unambiguous molecular replacement solution for > >> two copies/asymmetric unit of a 80 K protein for a crystal > >> integrated > >> in P212121 (R-merge around 9%) with a=101.8, b=132.2, c=138.9. > >> Refinement allowed rebuilding/completion of the model in the noraml way > >> but the R-free does not go below 30%. The map in the model regions looks > >> generally fine but there is a lot > >> of extra positive density in the solvent regions (some of it looking > >> like weak density for helices and strands) and unexpected positive > >> peaks within the model region. > >> Careful inspection allowed manual positioning of a completely different, > >> overlapping solution for the dimer which fits the extra density > >> perfectly. > >> The two incompatible solutions are related by a 2-fold axis parallel to > >> a. > >> This clearly suggests some kind of twinning. However twinning analysis > >> programmes (e.g. Phenix-Xtriage), while suggesting the potentiality > >> of pseudo-merohedral twinning (-h, l, k) do not reveal > >> any significant twinning fraction and proclaim the data likely to be > >> untwinned. (NB. The programmes do however highlight a > >> non-crystallographic translation and there are systematic intensity > >> differences in the data). Refinement, including this twinning law made > >> no difference > >> since the estimated twinning fraction was 0.02. Yet the extra density is > >> clearly there and I know exactly the real-space transformation between > >> the two packing solutions. > >> How can I best take into account this alternative solution (occupancy > >> seems to be around 20-30%) in the refinement ? > >> thanks for your suggestions > >> Stephen > >> > >> -- > >> > >> ********************************************************************** > >> Dr. Stephen Cusack, > >> Head of Grenoble Outstation of EMBL > >> Group leader in structural biology of protein-RNA complexes and viral > >> proteins > >> Joint appointment in EMBL Genome Biology Programme > >> Director of CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host > >> Cell Interactions (UVHCI) > >> ********************************************************************** > >> > >> Email: [log in to unmask] > >> Website: http://www.embl.fr > >> Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 > >> Fax: (33) 4 76 20 7199 > >> Postal address: EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP181, > >> 38042 Grenoble Cedex 9, France > >> Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, > >> 6 Rue Jules Horowitz, 38042 Grenoble, France > >> ********************************************************************** > >> > >> > > > > > Zbyszek Otwinowski > UT Southwestern Medical Center at Dallas > 5323 Harry Hines Blvd. > Dallas, TX 75390-8816 > Tel. 214-645-6385 > Fax. 214-645-6353 >