Hi Pramod, Can you post your merging statistics in different space groups, not just log files from scaling? These are summarised nicely by Scala or Aimless.
Also, have you tried indexing from different subsets of images? Perhaps there is a substantial contribution from a 'satellite' crystal in one orientation or crystal will be less split? I've had cases where I could not index properly if I had just used 0 and 90, but when I tried different subsets of images it worked. This is very easy to do in iMosflm. Andrew Leslie or other Mosflm developers, if they are reading this, might well be interested in looking at your images as they are currently interested in these kinds of problems with multiple lattices (see *Acta Cryst.* (2013). D*69*, 1195-1203) Eugene On 21 June 2013 21:58, Pramod Kumar <pramod...@gmail.com> wrote: > Dear ... > > Francis > > Last I remember, HKL2000 bases its indexing on the 'strongest' spots on an > image (though you could manually select spots). It could result in a > misindex if the strongest spots come from separate lattices.. > > I have used both HKL2000 and mosflm giving the same results (although I > have used manual selection of spots as a trial but results are identical). > > Try a program that uses all spots for indexing, across all images (XDS for > example) and you might get the true space group.. > > I have given several efforts to the XDS but its giving error "data image > of particular no. does not exist (initially it was saying 11th image than i > change image range then it says 21st and so on) *kindly check my data > collection profile and XDS.INP* file in attachment' > > > Or if the crystal is big enough, you could try shooting it in different > areas and 'searching' for a better spot to collect data. > Or 'grow a better crystal'. > > raising the crystals and struggle is on the peak... > > > Dear Eugene > > plz find the attached scale log file, scaling table of mosflm > > > When you index spots in Mosflm, do your predictions agree with the spots? > > plz see the snapshot of predicted spots.. > > > > Dear Eleanor > Yes both the molecule are visible in the ASU. > > > > Dear Pozharski > > Balbes pipeline hitting extremely high marks when fed into Phaser while > being complete nonsense (it's a 150kDa multi-domain protein and resulting > domain arrangement made absolutely no sense). Refinement was stuck with > high R-values and I sadly gave up on it for now. I suspected that refmac > step included in the pipeline artificially shifts the model so that it > conforms to Patterson map better, which results in high score in Phaser. > > My domain arrangement is as expected, two molecules in ASU. > > > thanks and regards > > pramod > > > > > > > > > > On Thu, Jun 20, 2013 at 3:50 PM, Eleanor Dodson <eleanor.dod...@york.ac.uk > > wrote: > >> As others say - the Rfactors look pretty good for MR, mine usually start >> over 50% even with a better model and one hopes they then decrease.. >> But you say you took the Balbes model into phaser? and I think Balbes >> automatically runs cycles of refinement so any comment on R factors may not >> mean much. >> >> Have you found both molecules in the asymmetric unit? You only give LLG >> for one? >> Eleanor >> >> >> >> >> On 19 June 2013 17:44, Eugene Valkov <eugene.val...@gmail.com> wrote: >> >>> Yes, I would agree with Francis that diffraction shows contribution from >>> several lattices, which could lead to misindexing. However, it should be >>> feasible to get a model that refines from this sort of data. >>> >>> Pramod - could you please post your data processing statistics from your >>> scaling program? Better if you have several for different spacegroups. >>> >>> Also, I have no idea how HKL200 does this, but could you please provide >>> an indexing solution table from Mosflm that shows penalties associated with >>> each type of space group? Was there a sharp penalty drop at some point or >>> was it more gradual? >>> >>> When you index spots in Mosflm, do your predictions agree with the >>> spots? Or is there a substantial portion that are missed? >>> >>> I would consider altering thresholds in Mosflm for indexing (see the >>> manual). >>> >>> Eugene >>> >>> >>> >>> >>> On 19 June 2013 17:34, Francis E. Reyes <francis.re...@colorado.edu>wrote: >>> >>>> On Jun 17, 2013, at 12:36 PM, Pramod Kumar <pramod...@gmail.com> wrote: >>>> >>>> >> I have a crystal data diffracted around 2.9 A*, >>>> >> during the data reduction HKL2000 not convincingly showed the space >>>> group (indexed in lower symmetry p1), while the mosflm given C-centered >>>> Orthorhombic, and again with little play around HKL2000 given CO >>>> > >>>> >>>> >>>> >>>> > no ice ring is appeared, diffraction pattern looks ok, misindexing in >>>> any direction is not conclusive to me (plz see the imj attachment) >>>> >>>> The diffraction does not look ok... there's hints of multiple >>>> lattices... which is not a problem if the two lattice orientations do not >>>> perfectly overlap (i.e. their spots are separable). >>>> >>>> Last I remember, HKL2000 bases its indexing on the 'strongest' spots on >>>> an image (though you could manually select spots). It could result in a >>>> misindex if the strongest spots come from separate lattices (and even worse >>>> if you have twinning/pseudosymmetry issues). >>>> >>>> Try a program that uses all spots for indexing, across all images (XDS >>>> for example) and you might get the true space group. >>>> >>>> Or if the crystal is big enough, you could try shooting it in different >>>> areas and 'searching' for a better spot to collect data. >>>> >>>> Or 'grow a better crystal'. >>>> >>>> F >>>> >>>> >>>> >>>> --------------------------------------------- >>>> Francis E. Reyes PhD >>>> 215 UCB >>>> University of Colorado at Boulder >>>> >>> >>> >>> >>> -- >>> Dr Eugene Valkov >>> MRC Laboratory of Molecular Biology >>> Francis Crick Avenue >>> Cambridge Biomedical Campus >>> Cambridge CB2 0QH, U.K. >>> >>> Email: eval...@mrc-lmb.cam.ac.uk >>> Tel: +44 (0) 1223 407840 >>> >> >> > > > -- > ************************************************ > Pramod Kumar. > Graduate Student. > Crystallography lab. > Department Of Biotechnology. > Indian Institute Of Technology Roorkee > Uttranchal.247667 > India > +919359189657. > ************************************************ > -- Dr Eugene Valkov MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. Email: eval...@mrc-lmb.cam.ac.uk Tel: +44 (0) 1223 407840
