Dear Eugene plz find the merging statics over this link
https://www.dropbox.com/sh/3155bp0c8axo7tx/0P1RWTTD8z?n=21758536 I have tried different subset of images for indexing, only cell edges are changing very marginal ( < 1 ) but no change in space group. Dear Manfred I have collected my data over mar345 detector, not present in detector type dropdown, how can I add. regards and thanks to all pramod On Mon, Jun 24, 2013 at 10:31 PM, Eugene Valkov <eugene.val...@gmail.com>wrote: > 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 > -- ************************************************ Pramod Kumar. Graduate Student. Crystallography lab. Department Of Biotechnology. Indian Institute Of Technology Roorkee Uttranchal.247667 India +919359189657. ************************************************
