Hi,
It solved my problem using the default parameters. Still, training
doesn't work.
The micrographs are normal but only motion correction seems to fail (eps
file attached)
Best,
Yashar
On 10/23/2018 11:34 AM, Takanori Nakane wrote:
> 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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--
Best,
Yashar Sadian
Christoph Mueller's group
Structural and computational Biology Unit
European Molecular Biology Laboratory (EMBL)
Meyerhofstrasse 1
69117 Heidelberg, Germany
Phone: 0049-6221-387-8496
Email: [log in to unmask]
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