[3dem] Issue with RelionRefine3D

[Sjors Scheres]

Hi Guillame,
Relion-3.0 will have this fixed. We're working hard on making this version
stable on other fronts now. More news soon.
Sjors


> This has happened to me a lot with one of my datasets, although always
> during class2D jobs (I am assuming it didn’t happen to me during class3D
> because at that stage I had already discarded the problematic particles).
> As I understand it, it is more likely to happen if your autopicking picked
> a lot of "junk". Using stricter settings for autopicking might help.
>
> The way I got rid of this error was to do a particle sorting right after
> extraction, and then select only the good particles. It can be difficult
> to tell the difference between good and bad particles, but after sorting
> if you look at the bad end you might be able to visually recognize obvious
> autopicking junk even with the very low contrast of the raw micrographs.
> Doing this consistently prevented the error from happening, but I am not
> very happy with this solution because I am sure I also threw away valid
> particles in the process.
>
> I wish relion would be able to automatically flag these problematic
> particles, ignore them during the current classification, and at the end
> provide a file listing them so the user can discard them from the dataset
> for subsequent jobs (this would require the "Select" job type to be able
> to do subtractions between two star files: subtract the flagged particles
> from the initial set of particles). That would be much more sensible and
> much less frustrating than the current behavior of crashing the job (I
> wasted so many hours of computer time because of this error…), and would
> make class2D an even better way of "cleaning" a dataset.
>
> Guillaume
>
>
>> On Mar 26, 2018, at 15:17, Vishaka Santosh <vs4p at virginia.edu> wrote:
>>
>> Hey, I know this issue has been asked recently, but I was wondering if
>> anyone had any idea as to how to resolve this.  I received this error
>> when attempting to run 3D auto-refine in Relion:
>>
>> Dumped data: error_dump_pdf_orientation, error_dump_pdf_orientation and
>> error_dump_unsorted.
>> slave 3 encountered error: ERROR:
>> No orientation was found as better than any other.
>>
>> A particle image was compared to the reference and resulted in all-zero
>> weights (for all orientations). This should not happen, unless your data
>> has very special characteristics. This has historically happened for
>> some
>> lower-precision calculations, but multiple fallbacks have since been
>> implemented. Please report this error to the relion developers at
>>
>>              github.com/3dem/relion/issues
>> <http://github.com/3dem/relion/issues>
>>
>> File:
>> /programs/x86_64-linux/relion/2.1_cu8.0/src/gpu_utils/cuda_ml_optimiser.cu
>> <http://cuda_ml_optimiser.cu/> line: 1710
>>
>> Does anyone have any idea as to what might cause this and any fixes?
>>
>> --
>> Vishaka Santosh
>> UVA Class of 2011, BS in Chemistry with a specialization in Biochemistry
>> VCU Class of 2013, MS in Biochemistry
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>
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-- 
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