Re: [scipion-users] relion classification of xmipp binned particles

[ldelcano <lde...@cn...>]

Hi Jose Miguel,

I have tested with a project that I have. Particles 200 px resized to 66 
px (factor 0.333) and normalized with Xmipp. Then I run Relion 2D 
classification and it arrives to Iteration 1 without errors.  I guess 
the error that Juha is reporting is on Estimating Initial Noise 
Expectra. I will try tomorrow with another dataset.

cheers

Laura


On 27/06/17 15:03, Jose Miguel de la Rosa Trevin wrote:
> Laura, have you checked if the same error happens (or not) with a 
> tutorial dataset, for example?
>
> On Tue, Jun 27, 2017 at 3:02 PM, Laura del Caño 
> <su...@bc... <mailto:su...@bc...>> 
> wrote:
>
>     Hi Juha,
>
>     could you send us protocol parameters for the binning and
>     normalization, as well as particle size (and maybe logs) to try to
>     reproduce the problem?
>
>     thanks
>     Laura
>
>
>         Activo Mar, 27 Junio at 1:21 PM , Juha Huiskonen
>         <ju...@st... <mailto:ju...@st...>> Escrito:
>         Dear all,
>
>         I need to run a fairly large classification run. To speed it
>         up, I have run xmipp-crop/resize particles to achieve binning
>         by factor of 3 and then normalised the particles again with
>         xmipp-preprocess particles.
>
>         Without binning/renormalization the job runs fine (albeit
>         slowly). With binning/renormalization I get a segmentation
>         fault referring to libfftw3 right when the 'Estimating initial
>         noise spectra' starts. I am running on GPU.
>
>         The only difference I can see between the two is that after
>         binning/renormalization all the particles are in one large
>         stack, whereas normally they are in several separate stacks.
>         Has anyone else seen this behaviour? Any suggestions?
>
>         Best wishes,
>         Juha
>
>     168:553135
>
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