Hi Pranav,
As others correctly pointed out the localized reconstruction script still
requires relion 1.4 (after you have created and extracted the sub-particles
you can proceed with any version).
We are working to remove any references to 1.4 but in the meanwhile having
relion 1.4 in the path is the only easy option (indeed it’s the part where
the symmetry operators are printed from relion that is causing the
problem).
Best wishes,
Juha
On Sat, 9 Jun 2018 at 21:18, Kyle Morris <[log in to unmask]> wrote:
> OK Pranav, that’s a problem, these are likely only intermediate files
> before it does the actual subparticle extraction.
>
> I think Juha and Serban are going to know how to help you :) but I really
> think the issue is happening when localrec is trying to get the symmetry
> operators from relion_refine. You should make sure you can run the command
> that threw the error in a new terminal in isolation and continue
> troubleshooting from there. It was:
>
> relion_refine --sym I1 --print_symmetry_ops --o ./ > relion_symops.tmp
>>>
>>
> Good luck! Happy to talk more offline.
>
> Cheers,
> Kyle
>
> On 9 Jun 2018, at 11:01, Pranav Shah <[log in to unmask]> wrote:
>
> Hi Grigory Hi Kyle,
>
> Thanks for your input. I will see how i can work around relion version
> incompatibility.
> I have a particles.star file in the output folder, However, when i took a
> look at some of the mrc files, the images appear to be that of the full
> virus and not the sub-particles.
> I wonder if this will have implications on the downstream processing.
>
> On Sat, Jun 9, 2018 at 12:13 PM, Kyle Morris <[log in to unmask]>
> wrote:
>
>> Hi Pranav,
>>
>> I use localised reconstruction extensively, it’s really great. I source
>> rln1.4 for the subparticle extraction using scipion & localrec scripts
>> (from github) and once I’ve got the star and mrc stacks use these in
>> rln2.1.
>>
>> I will look again at your error more closely but at first glance it seems
>> to crash out when trying to get symmetry operators from relion_refine. I
>> don’t see this operation in my workflow but that looks like where it’s
>> going wrong for you...
>>
>> If you’ve got your subparticles and your star file for them then you have
>> everything you need to proceed in Relion 2.1, did it make a star file?
>>
>> Best wishes,
>> Kyle
>>
>> On 9 Jun 2018, at 08:31, Gregory Sharov <[log in to unmask]> wrote:
>>
>> Hello Pranav,
>>
>> as far as I know, relion2 is not supported by localrec scripts. You will
>> have to use relion-1.4
>>
>> 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 <+44%201223%20267542>
>> e-mail: [log in to unmask]
>>
>> On Sat, Jun 9, 2018 at 4:15 PM, Pranav Shah <[log in to unmask]> wrote:
>>
>>> Hi Juha, Hi Serban,
>>>
>>> I was trying to perform a localised reconstruction on my virus particles
>>> based off of the mini-tutorial on the wiki. I ran the program with the
>>> follwoing parameters:
>>>
>>> scipion run relion_localized_reconstruction.py
>>> Refine3D/job015/run_ct3_data.star --prepare_particles --create_subparticles
>>> --extract_subparticles --sym I1 --vector 0.000,0.618,1.000 --length 80
>>> --angpix 1.065 --particle_size 350 --subparticle_size 80 --j 8 --np 4
>>> --output Particles
>>>
>>> while the program sucessfully created a Particles folder with several
>>> thousand mrc files it exited with the follwoing error:
>>>
>>> Creating subparticles...
>>> ~~~~** Running command: relion_refine --sym I1 --print_symmetry_ops --o
>>> ./ > relion_symops.tmp
>>> The following errors were encountered upon command-line parsing:
>>> ERROR: Argument --i not found or invalid argument
>>> ERROR:
>>> Errors encountered on the command line (see above), exiting...
>>> File:
>>> /programs/x86_64-linux/scipion/1.2/software/em/relion-2.1/src/ml_optimiser.cpp
>>> line: 1286
>>> Traceback (most recent call last):
>>> File
>>> "/programs/x86_64-linux/scipion/1.2/software/em/localrec-1.2.0/relion_localized_reconstruction.py",
>>> line 252, in <module>
>>> LocalizedReconstruction().main()
>>> File
>>> "/programs/x86_64-linux/scipion/1.2/software/em/localrec-1.2.0/relion_localized_reconstruction.py",
>>> line 206, in main
>>> symmetry_matrices = matrix_from_symmetry(args.sym)
>>> File
>>> "/programs/x86_64-linux/scipion/1.2/software/em/localrec-1.2.0/lib/localrec/matrix3.py",
>>> line 150, in matrix_from_symmetry
>>> relion_create_symmetry_ops_file(symString, tmpSymFile)
>>> File
>>> "/programs/x86_64-linux/scipion/1.2/software/em/localrec-1.2.0/lib/localrec/matrix3.py",
>>> line 160, in relion_create_symmetry_ops_file
>>> runProgram('relion_refine', '--sym %s --print_symmetry_ops --o ./ >
>>> %s' % (symString, filename))
>>> File
>>> "/nfs/sbgrid/programs/x86_64-linux/scipion/1.2/pyworkflow/em/__init__.py",
>>> line 185, in runProgram
>>> pwutils.runJob(None, program, params, env=env)
>>> File
>>> "/nfs/sbgrid/programs/x86_64-linux/scipion/1.2/pyworkflow/utils/process.py",
>>> line 51, in runJob
>>> return runCommand(command, env, cwd)
>>> File
>>> "/nfs/sbgrid/programs/x86_64-linux/scipion/1.2/pyworkflow/utils/process.py",
>>> line 65, in runCommand
>>> check_call(command, shell=True, stdout=sys.stdout,
>>> stderr=sys.stderr, env=env, cwd=cwd)
>>> File
>>> "/nfs/sbgrid/programs/x86_64-linux/scipion/1.2/software/lib/python2.7/subprocess.py",
>>> line 186, in check_call
>>> raise CalledProcessError(retcode, cmd)
>>> subprocess.CalledProcessError: Command 'relion_refine --sym I1
>>> --print_symmetry_ops --o ./ > relion_symops.tmp' returned non-zero exit
>>> status 1
>>>
>>> I tried to rerun the program with a --create_star flag, but it seems
>>> this function has been deprecated in the latest version of the program.
>>> Could you please help me with figuring out how i can work around this
>>> error?
>>>
>>> Cheers,
>>> Pranav
>>>
>>> --
>>> Pranav Shah
>>> Postdoctoral Research Fellow.
>>>
>>> Hogle Lab
>>> Harvard Medical School
>>> 240 Longwood Avenue
>>> <https://maps.google.com/?q=240+Longwood+Avenue+Boston,+MA+02115&entry=gmail&source=g>
>>> Boston, MA 02115
>>> <https://maps.google.com/?q=240+Longwood+Avenue+Boston,+MA+02115&entry=gmail&source=g>
>>> (617) 432-4360 (fax)
>>> (617) 432-3839 (lab)
>>>
>>> ------------------------------
>>>
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>>>
>>
>>
>> ------------------------------
>>
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>>
>>
>
>
> --
> Pranav Shah
>
>
>
> ------------------------------
>
> To unsubscribe from the CCPEM list, click the following link:
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>
--
Juha T. Huiskonen, PhD
Associate Professor
Principal Investigator
Head of Oxford Particle Imaging Centre
Division of Structural Biology
University of Oxford
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