Re: [scipion-users] Xmipp viewer issue

[Erik Ž. <eri...@gm...>]

Hi David,

I am not receiving any error messages from Scipion after the command.
However, there is no new window popping out after the command.

Erik Zupa


On Mon, Jul 9, 2018 at 12:24 PM, David Maluenda <dma...@cn...>
wrote:

> 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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> 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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