Re: [scipion-users] relion 3D_auto-refine

[Grigory S. <sha...@gm...>]

Hello Dmitry,

are you using release-1.1.1 branch from git? If you do movie processing in
Relion, inputs are movie particles (extracted using a separate protocol)
and a completed 3d auto-refine run with normal particles. Is this the case?
This error could happen only if your normal particles after relion
auto-refine 3d run do not have any shift information...

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: gs...@mr...

On Thu, Sep 7, 2017 at 2:08 PM, D.A. Semchonok <sem...@gm...> wrote:

> Dear colleagues,
>
> I have a new issue running the relion 3d auto refinement -
>
> so
> - the input are the movies;
> - *Select previous run* the result of relion 3d auto-refine (with stacked
> frames)
>
>
>
> the error
>
> Converting set from 'Runs/032578_XmippProtExtractMovieParticles/movie_particles.sqlite'
> into 'Runs/032753_ProtRelionRefine3D/movie_particles.star'
> 00081:   Traceback (most recent call last):
> 00082:     File "/home/p260888/scipion/pyworkflow/protocol/protocol.py",
> line 182, in run
> 00083:       self._run()
> 00084:     File "/home/p260888/scipion/pyworkflow/protocol/protocol.py",
> line 228, in _run
> 00085:       resultFiles = self._runFunc()
> 00086:     File "/home/p260888/scipion/pyworkflow/protocol/protocol.py",
> line 224, in _runFunc
> 00087:       return self._func(*self._args)
> 00088:     File "/home/p260888/scipion/pyworkflow/em/packages/relion/protocol_base.py",
> line 805, in convertInputStep
> 00089:       mdAux.copyColumn(md.RLN_ORIENT_ORIGIN_X_PRIOR,
> md.RLN_ORIENT_ORIGIN_X)
> 00090:   XmippError: Source label: 'rlnOriginX' doesn't exist on metadata
> 00091:   Protocol failed: Source label: 'rlnOriginX' doesn't exist on
> metadata
> 00092:   FAILED: convertInputStep, step 1
> 00093:     2017-09-07 14:57:39.324748
> 00094:   ------------------- PROTOCOL FAILED (DONE 1/3)
>
>
> Suggestions?
>
> Thank you!
>
> Sincerely,
> Dmitry
>
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