Re: [scipion-users] Xmipp viewer issue

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

Ouch.. strange..

What appears as Output for the Xmipp-ExtractParticles? Could the output set
be empty?
The summary tab (in the scipion GUI) should display:

*Name-of-the-protocol* -> outputParticles            SetOfParticles (* #
items*, ** x **, **.* A/px )

Then, the number of items # is bigger than 0?

​ <http://ucm.es/>

*_____Dr. David Maluenda Niubó*
dma...@cn... - (+34) 619 029 310
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 1:23 PM Erik Župa <eri...@gm...> wrote:

> 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*
>> dma...@cn... - (+34) 619 029 310
>> CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es>
>> BioComputing Unit <http://biocomputingunit.es/>
>>
>> This email message and any documents attached to it may contain
>> confidential or legally protected material and are intended solely for the
>> use of the individual or organization to whom they are addressed. We remind
>> you that if you are not the intended recipient of this email message or the
>> person responsible for processing it, then you are not authorized to read,
>> save, modify, send, copy or disclose any of its contents. If you have
>> received this email message by mistake, we kindly ask you to inform the
>> sender of this and to eliminate both the message and any attachments it
>> carries from your account. Thank you for your collaboration.
>>
>>
>>
>> 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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>>
>