Hi,

Thank you very much for feedback.

> I wonder if this was the reason that I encountered the previous problem,

Yes.

> and how should I inspect the movies?

Please look at motion corrected micrographs from them.
Does anything look suspicious?
Examples include: empty (blank) micrograph, out of focus image,
 detector glitches (lots of hot/cold pixels, stripes, black patches, etc)
 failed motion correction (polynomial fitting can diverge and
 produce strange patterns)

We are trying to stabilize Bayesian Polishing but don't know
what causes NaNs yet.

Best regards,

Takanori Nakane

> Hi Jasenko and Takanori,
>
> Thanks so much for the commits, I am now able to have two of my datasets
> to finish polishing and output shiny.star files. In both cases I have a
> small portion (6 out of 5500 and 105 out of 7500 movies) having the
> following message in the run.err file:
>
> NaNs detected in
> Polish/job033/Movies/FoilHole_8023171_Data_8019792_8019793_20180908_1922!
> Please inspect this movie.
>
> I wonder if this was the reason that I encountered the previous problem,
> and how should I inspect the movies? Sorry if similar questions have
> already been answered in previous topics. Thanks again for your help!
> Best,
>
> Zhaoming Su, Ph.D.
>
> Research Scientist, Bioengineering
>
> Stanford University
>
> ________________________________
> From: Collaborative Computational Project in Electron cryo-Microscopy
> <[log in to unmask]> on behalf of Takanori Nakane
> <[log in to unmask]>
> Sent: Friday, October 19, 2018 11:15:49 AM
> To: [log in to unmask]
> Subject: Re: [ccpem] Bayesian Polishing b-factor fitting error
>
> Hi,
>
> Jasenko made two more commits (0ad988f, 294ce0d) after I posted
> here yesterday. Did you try that? If the problem persists,
> we need more time to investigate. This is not an easy bug to fix.
>
> Best regards,
>
> Takanori Nakane
>
> On 2018/10/19 17:37, Leonid Sazanov wrote:
>> Dear all,
>>
>> We tried this fix, but still get the same error at the same frame.
>> Please let us know what else can be tried.
>>
>> Many thanks,
>> Leonid
>>
>> Prof. Leonid Sazanov
>> IST Austria
>> Am Campus 1
>> A-3400 Klosterneuburg
>> Austria
>>
>> Phone: +43 2243 9000 3026
>> E-mail: [log in to unmask]
>> Web: https://ist.ac.at/research/life-sciences/sazanov-group/

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