Re: [scipion-users] Xmipp viewer issue

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In ~/.config/scipion/scipion.conf there is a line pointing to scipion
EM_ROOT folder (you should adjust version name to the one you have), i.e.:
RELION_HOME=%(EM_ROOT)s/relion-1.4

It points to scipion/software/em/relion-1.4 which could be a symbolic link
to whatever path you have installed relion.

Please have a look at
https://github.com/I2PC/scipion/wiki/Installing-EM-Packages#linking-to-existing-package-installations

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542
e-mail: gs...@mr...

On Thu, Jul 12, 2018 at 1:01 PM Erik Župa <eri...@gm...> wrote:

> My config file is totally missing RELION_HOME despite the relion package
> was installed. How do I set RELION_HOME?
>
> Erik Zupa
>
> On Thu, Jul 12, 2018 at 1:28 PM, Gregory Sharov <sha...@gm...>
> wrote:
>
>> Hi Erik,
>>
>> It looks like 'which relion_refine_mpi' returns  nothing. Do you have a
>> correct RELION_HOME set in config file? Did you try running relion with mpi
>> outside of scipion?
>>
>> On Thu, Jul 12, 2018, 12:04 Erik Župa <eri...@gm...> wrote:
>>
>>> I solved the problem of particle extraction window. It was wrong Java
>>> path. However, my relion 2D classification is not working, Scipion is
>>> showing  this Error
>>>
>>> Erik Zupa
>>>
>>> 00021:   mpirun: Error: unknown option "--tau2_fudge"
>>> 00022:   Type 'mpirun --help' for usage.
>>> 00023:   Traceback (most recent call last):
>>> 00024:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>> line 182, in run
>>> 00025:       self._run()
>>> 00026:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>> line 228, in _run
>>> 00027:       resultFiles = self._runFunc()
>>> 00028:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>> line 224, in _runFunc
>>> 00029:       return self._func(*self._args)
>>> 00030:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/em/packages/relion/protocol_base.py",
>>> line 789, in runRelionStep
>>> 00031:       self.runJob(self._getProgram(), params)
>>> 00032:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/protocol.py",
>>> line 1077, in runJob
>>> 00033:       self._stepsExecutor.runJob(self._log, program, arguments,
>>> **kwargs)
>>> 00034:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/protocol/executor.py",
>>> line 56, in runJob
>>> 00035:       env=env, cwd=cwd)
>>> 00036:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
>>> line 51, in runJob
>>> 00037:       return runCommand(command, env, cwd)
>>> 00038:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/pyworkflow/utils/process.py",
>>> line 65, in runCommand
>>> 00039:       check_call(command, shell=True, stdout=sys.stdout,
>>> stderr=sys.stderr, env=env, cwd=cwd)
>>> 00040:     File
>>> "/home/erikzupa/Downloads/scipion_v1.1_2017-06-14_linux64/scipion/software/lib/python2.7/subprocess.py",
>>> line 540, in check_call
>>> 00041:       raise CalledProcessError(retcode, cmd)
>>> 00042:   CalledProcessError: Command 'mpirun -np 3 -bynode  `which
>>> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
>>> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
>>> Runs/003210_ProtRelionClassify2D/extra/relion --i
>>> Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
>>> 210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
>>> --zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
>>> status 213
>>> 00043:   Protocol failed: Command 'mpirun -np 3 -bynode  `which
>>> relion_refine_mpi` --tau2_fudge 2 --scale  --iter 25 --norm
>>> --memory_per_thread 2 --ctf  --offset_range 5.0 --oversampling 1 --o
>>> Runs/003210_ProtRelionClassify2D/extra/relion --i
>>> Runs/003210_ProtRelionClassify2D/input_particles.star --particle_diameter
>>> 210.0 --K 3 --psi_step 10.0 --ctf_phase_flipped  --flatten_solvent
>>> --zero_mask  --offset_step 2.0 --angpix 3.0  --j 1' returned non-zero exit
>>> status 213
>>>
>>> On Tue, Jul 10, 2018 at 12:01 PM, Pablo Conesa <pc...@cn...>
>>> wrote:
>>>
>>>> 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... - (+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 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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>>>>>>>
>>>>>>
>>>>>
>>>>
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Re: [scipion-users] Xmipp viewer issue

Image processing framework to integrate EM software packages.

Re: [scipion-users] Xmipp viewer issue