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
>>
>>
>
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