Re: [scipion-users] Xmipp viewer issue

[Pablo C. <pc...@cn...>]

is java in your path?

what happens if you type in the "console/terminal":

java -version


On 09/07/18 14:39, David Maluenda wrote:
> 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... <mailto: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... 
> <mailto: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... <mailto: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... <mailto: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...
>         <mailto: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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