I tried removing micrographs with small defoci, but still get the error below: Expectation iteration 3 of 50 000/??? sec ~~(,_,"> [oo] exp_thisparticle_sumweight= nan exp_thisparticle_sumweight= nan exp_thisparticle_sumweight= nan exp_thisparticle_sumweight= nan exp_thisparticle_sumweight= nan exp_thisparticle_sumweight= nan exp_thisparticle_sumweight= nan exp_thisparticle_sumweight= nan exp_thisparticle_sumweight= nan exp_thisparticle_sumweight= nan exp_part_id= 111316exp_iimage=1 group_id= 1765 mymodel.scale_correction[group_id]= nan exp_ipass= 0 sampling.NrDirections(0, true)= 48 sampling.NrDirections(0, false)= 48 sampling.NrPsiSamplings(0, true)= 12 sampling.NrPsiSamplings(0, false)= 12 mymodel.sigma2_noise[exp_ipart]= 0.00015 4.7e-05 4.7e-05 3.9e-05 3.7e-05 . . . 0 0 0 exp_thisparticle_sumweight= 0 nan 0 0 0 0 0 0 0 0 0 0 mymodel.avg_norm_correction= 0.671374 wsum_model.avg_norm_correction= 0 written out Mweight.spi exp_thisparticle_sumweight= nan exp_min_diff2[exp_ipart]= 9.9e+100 slave 40 encountered error: ERROR!!! zero sum of weights.... File: src/ml_optimiser.cpp line: 3938 +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ -- Amedee des Georges Frank lab Howard Hughes Medical Institute Dept. of Biochemistry and Molecular Biophysics 650 W 168th St, P&S Black Building room 221 New York, NY 10032 (T) 212 305-9527 (F) 212 305-9500 (E) [log in to unmask] http://franklab.cpmc.columbia.edu On Oct 4, 2013, at 2:34 PM, Amedee des Georges <[log in to unmask]> wrote: > Here is what I get after changing > > mymodel.scale_correction[igroup] = 0.; > to: > mymodel.scale_correction[igroup] = 1.; > > WARNING: ignoring group 845 with very small or negative scale (6.91088e-310); Use larger groups for more stable scale estimates. > WARNING: ignoring group 2035 with very small or negative scale (6.94752e-310); Use larger groups for more stable scale estimates. > WARNING: ignoring group 1094 with very small or negative scale (6.94713e-310); Use larger groups for more stable scale estimates. > WARNING: ignoring group 2403 with very small or negative scale (6.93112e-310); Use larger groups for more stable scale estimates. > > It seem to be doing this for the whole dataset. > > > > On Oct 4, 2013, at 10:58 AM, Sjors Scheres <[log in to unmask]> wrote: > >> Hi Amedee, >> Did you do this? >> http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Known_issue >> S >> >> On 10/04/2013 03:07 PM, Amedee des Georges wrote: >>> As I feared, the problem persists with the official release. I suspect some of the micrographs to have very low SNR and trigger this bug. >>> >>> >>> >>> Expectation iteration 2 of 50 >>> 52.70/52.70 min ............................................................~~(,_,"> >>> Maximization ... >>> 9/ 9 sec ............................................................~~(,_,"> >>> Estimating accuracies in the orientational assignment ... >>> 1.42/1.42 min ............................................................~~(,_,"> >>> Auto-refine: Estimated accuracy angles= 23.18 degrees; offsets= 5.775 pixels >>> Auto-refine: WARNING: The angular accuracy is worse than 10 degrees, so basically you cannot align your particles (yet)! >>> Auto-refine: WARNING: You probably need not worry if the accuracy improves during the next few iterations. >>> Auto-refine: WARNING: However, if the problem persists it may lead to spurious FSC curves, so be wary of inflated resolution estimates... >>> Auto-refine: WARNING: Sometimes it is better to tune resolution yourself by adjusting T in a 3D-classification with a single class. >>> Estimated required memory for expectation step= 0.384728 Gb, maximum allowed memory = 8 Gb. >>> CurrentResolution= 31.688 Angstroms, which requires orientationSampling of at least 11.25 degrees for a particle of diameter 320 Angstroms >>> Oversampling= 0 NrHiddenVariableSamplingPoints= 74880 >>> OrientationalSampling= 30 NrOrientations= 576 >>> TranslationalSampling= 6 NrTranslations= 13 >>> ============================= >>> Oversampling= 1 NrHiddenVariableSamplingPoints= 2396160 >>> OrientationalSampling= 15 NrOrientations= 4608 >>> TranslationalSampling= 3 NrTranslations= 52 >>> ============================= >>> Expectation iteration 3 of 50 >>> 000/??? sec ~~(,_,"> [oo] exp_thisparticle_sumweight= nan >>> exp_thisparticle_sumweight= nan >>> exp_thisparticle_sumweight= nan >>> exp_thisparticle_sumweight= nan >>> exp_thisparticle_sumweight= nan >>> exp_thisparticle_sumweight= nan >>> exp_thisparticle_sumweight= nan >>> exp_thisparticle_sumweight= nan >>> exp_thisparticle_sumweight= nan >>> exp_thisparticle_sumweight= nan >>> exp_thisparticle_sumweight= nan >>> >>> On Oct 3, 2013, at 3:12 AM, Sjors Scheres <[log in to unmask]> wrote: >>> >>>> Dear Amedee, >>>> Please first update to the official relion-1.2 release. The beta-releases >>>> may well contain bugs. >>>> best, S >>>> >>>>> >>>>> Hi, >>>>> >>>>> I have an unusual error at the 3rd iteration of classification on a new >>>>> dataset. This happens as the resolution dropped from 80 to 30A at the >>>>> previous iteration. >>>>> >>>>> Expectation iteration 3 of 50 >>>>> 000/??? sec ~~(,_,"> >>>>> [oo] exp_thisparticle_sumweight= nan >>>>> exp_thisparticle_sumweight= nan >>>>> exp_thisparticle_sumweight= nan >>>>> exp_thisparticle_sumweight= nan >>>>> exp_thisparticle_sumweight= nan >>>>> exp_thisparticle_sumweight= nan >>>>> exp_thisparticle_sumweight= nan >>>>> >>>>> I didn't manage to fix, so any help is welcome. This is with relion 1.2b7, >>>>> which was running fine until now. >>>>> >>>>> Amedee >>>>> >>>>> >>>> >>>> -- >>>> Sjors Scheres >>>> MRC Laboratory of Molecular Biology >>>> Francis Crick Avenue, Cambridge Biomedical Campus >>>> Cambridge CB2 0QH, U.K. >>>> tel: +44 (0)1223 267061 >>>> http://www2.mrc-lmb.cam.ac.uk/groups/scheres >>>> >>>> >> >> -- >> Sjors Scheres >> MRC Laboratory of Molecular Biology >> Francis Crick Avenue, Cambridge Biomedical Campus >> Cambridge CB2 0QH, U.K. >> tel: +44 (0)1223 267061 >> http://www2.mrc-lmb.cam.ac.uk/groups/scheres >> >> >