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
>
>
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