Re: [scipion-users] Xmipp viewer issue

[David M. <dma...@cn...>]

Hi Erik,

This is the command that Scipion launch to open the viewer and it looks
fine.. so, it should open a window with the particles...

Is there any error message after the command that you are reporting?

Thanks!

​ <http://ucm.es/>

*_____Dr. David Maluenda Niubó*
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CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
BioComputing Unit <http://biocomputingunit.es/>

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On Mon, Jul 9, 2018 at 11:39 AM Erik Župa <eri...@gm...> wrote:

> Hello colleagues,
>
>
> I have problem to analyze results of extracting of particles. I
> successfully ran xmipp3- extract particles. However, I cannot analyze
> results because everytime I try, Scipion come with something like this:
>
>
> java -Xmx2g -d64
> -Djava.library.path=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/lib
> -Dplugins.dir=/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/plugins
> -cp
> /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-3.b10.fc26.x86_64/lib/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/external/imagej/*:/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/em/xmipp/java/lib/*
> xmipp.viewer.scipion.ScipionViewer -i
> "Runs/002809_XmippProtExtractParticles/particles.sqlite" --visible id
> enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR _sampling
> _ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle
> _transform._matrix --order id enabled _index _filename _xmipp_zScore
> _xmipp_cumulativeSSNR _sampling _ctfModel._defocusU _ctfModel._defocusV
> _ctfModel._defocusAngle _transform._matrix --render _filename --sortby
> _xmipp_zScore asc --scipion 55971 2856
>
>
> I am thankful for any help.
>
> Erik Zupa
>
> CEITEC Brno Czech Republic
>
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