Hi,
As the error message says, particle stacks must have
the extension of .mrcs not .mrc.
Best regards,
Takanori Nakane
On 2020/01/04 22:01, eswar reddy wrote:
> Hi Takanori,
>
> Thanks for pointing out about the relion_convert command, now I directly
> imported star file in to relion and tried to run a 3D classification,
> but more or less I got the same error as previous.
>
> Even though I have made the symlink for the particle images; it seems
> the relion can't find the path in to the extract job of cryosparc.
>
> WARNING: J42relion.star seems to be from a previous version of Relion.
> Attempting conversion...
> You should make sure metadata in the optics group table after
> conversion is correct.
> in: /home/software/cryoem/relion/src/image.h, line 1399
> ERROR:
> Image::read ERROR: stacks of images in MRC-format should have extension
> .mrcs; .mrc extensions are reserved for 3D maps.
> Warning:
> [log in to unmask]
> not found.
> Warning: Not all image files could be found.
> Image sizes and dimensionalities will be missing from the star file.
> Later steps (e.g. re-extraction, CtfRefine) can fail!!
> Repeat this job after fixing the image paths.
> WARNING: input particles STAR file does not have a column for image
> dimensionality, assuming 2D images ...
> in: /home/software/cryoem/relion/src/jaz/obs_model.cpp, line 688
> ERROR:
> ObservationModel::getBoxSize: box sizes not available. Make sure
> particle images are available before converting/importing STAR files
> from earlier versions of RELION.
> === Backtrace ===
> /usr/local/relion/bin/relion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41)
> [0x434671]
> /usr/local/relion/bin/relion_refine(_ZNK16ObservationModel10getBoxSizeEi+0x6b)
> [0x4fcd0b]
> /usr/local/relion/bin/relion_refine(_ZN7MlModel20initialiseFromImagesE8FileNamebR10ExperimentRbS3_S3_dbb+0xc9)
> [0x60c499]
> /usr/local/relion/bin/relion_refine(_ZN11MlOptimiser17initialiseGeneralEi+0x4ff)
> [0x4827ef]
> /usr/local/relion/bin/relion_refine(_ZN11MlOptimiser10initialiseEv+0x2f)
> [0x48522f]
> /usr/local/relion/bin/relion_refine(main+0x33) [0x427bc3]
> /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f0d80b02505]
> /usr/local/relion/bin/relion_refine() [0x42865f]
> ==================
> ERROR:
> ObservationModel::getBoxSize: box sizes not available. Make sure
> particle images are available before converting/importing STAR files
> from earlier versions of RELION.
>
> # version 30001
>
> data_optics
>
> loop_
> _rlnOpticsGroup #1
> _rlnOpticsGroupName #2
> _rlnAmplitudeContrast #3
> _rlnSphericalAberration #4
> _rlnVoltage #5
> _rlnImagePixelSize #6
> 1 opticsGroup1 0.100000 2.700000 200.000000
> 1.128000
>
>
> # version 30001
>
> data_particles
>
> loop_
> _rlnImageName #1
> _rlnMicrographName #2
> _rlnCoordinateX #3
> _rlnCoordinateY #4
> _rlnAnglePsi #5
> _rlnDefocusU #6
> _rlnDefocusV #7
> _rlnDefocusAngle #8
> _rlnPhaseShift #9
> _rlnCtfBfactor #10
> _rlnOpticsGroup #11
> _rlnRandomSubset #12
> _rlnClassNumber #13
> _rlnOriginXAngst #14
> _rlnOriginYAngst #15
> [log in to unmask]
> J2/motioncorrected/29657447_20190831_0031_patch_aligned_doseweighted.mrc
> 1272.000000 1000.000000 201.122437 10637.148438 10467.870117
> -0.18420 0.000000 0.000000 1 1
> 63 5.499000 8.431800
> [log in to unmask]
> J2/motioncorrected/29657447_20190831_0031_patch_aligned_doseweighted.mrc
> 2192.000000 552.000000 157.040802 10707.245117 10537.966797
> -0.18420 0.000000 0.000000 1 1
> 159 0.366600 -7.69860
>
> what might be wrong
> Best,
> E.R
>
>
>
>
>
>
> On Tue, 31 Dec 2019 at 15:32, Takanori Nakane <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi,
>
> What you showed is the particle.star after Import, right?
> Then you don't have to run relion_convert_star.
>
> Takanori
>
> On 2019/12/31 17:20, eswar reddy wrote:
> > Hi Takanori,
> > Thanks for your reply,
> > This is what I need after reading your email,
> > Created a symlink for the relion to access the particles images that
> > have been extracted in cryosparc; then imported the .star file
> that has
> > been converted using CS command and below is the header of the
> star file
> > # version 30001
> >
> > data_optics
> >
> > loop_
> > _rlnOpticsGroup #1
> > _rlnOpticsGroupName #2
> > _rlnAmplitudeContrast #3
> > _rlnSphericalAberration #4
> > _rlnVoltage #5
> > _rlnImagePixelSize #6
> > 1 opticsGroup1 0.100000 2.700000 200.000000
> > 1.128000
> >
> >
> > # version 30001
> >
> > data_particles
> >
> > loop_
> > _rlnImageName #1
> > _rlnMicrographName #2
> > _rlnCoordinateX #3
> > _rlnCoordinateY #4
> > _rlnAnglePsi #5
> > _rlnDefocusU #6
> > _rlnDefocusV #7
> > _rlnDefocusAngle #8
> > _rlnPhaseShift #9
> > _rlnCtfBfactor #10
> > _rlnOpticsGroup #11
> > _rlnRandomSubset #12
> > _rlnClassNumber #13
> > _rlnOriginXAngst #14
> > _rlnOriginYAngst #15
> >
> [log in to unmask]
>
> >
> J2/motioncorrected/29657447_20190831_0031_patch_aligned_doseweighted.mrc
>
> > 1272.000000 1000.000000 201.122437 10637.148438 10467.870117
> > -0.18420 0.000000 0.000000 1 1
> > 63 5.499000 8.431800
> >
> > /but when I use
> > /
> > /relion_convert_star --i J44_par4relion.star --o J44tst.star/
> > /The input is a micrograph STAR file with CTF information.
> > Written J44tst.star
> > Please carefully examine the optics group table at the beginning
> of the
> > output to make sure the information is correct./
> > *but the Output star file is empty !!.*
> > /If I use the output of csparc2star.py star I keep getting the
> Boxsize
> > error as we discussed earlier. /
> >
> > What might went wrong.
> >
> > Best,
> > E.R
> >
> >
> > On Mon, 30 Dec 2019 at 18:39, Takanori Nakane
> <[log in to unmask] <mailto:[log in to unmask]>
> > <mailto:[log in to unmask]
> <mailto:[log in to unmask]>>> wrote:
> >
> > Hi,
> >
> > Does csparc2star.py output in RELION 3.0 format, or 3.1 format?
> >
> > If it is 3.0 format, make sure particle images are available
> > before importing the file or running relion_convert_star.
> > Otherwise, 3.0-to-3.1 conversion cannot fill the box size and the
> > dimensionality fields.
> >
> > If it is 3.1 format, make sure the optics table in the
> > STAR file contains "_rlnImageSize" item (box size in pixels)
> > and "_rlnImageDimensionality" (should be 2 for SPA).
> >
> > Best regards,
> >
> > Takanori Nakane
> >
> > On 2019/12/30 23:34, eswar reddy wrote:
> > > Dear all,
> > > I keep getting error in relion 3.1; when I tried to run a 3D
> > > classification job using the particles that have been
> extracted
> > and 2D
> > > classified in cryosparc, I have used csparc2star.py command to
> > convert
> > > cs file to star file. I have supplemented the generated
> star file
> > and a
> > > reference map that I have obtained from Ab-initio
> classification of
> > > cryosparc to do a 3D job in relion
> > > *
> > > *
> > > *WARNING: input particles STAR file does not have a column
> for image
> > > dimensionality, assuming 2D images ...
> > > in: /home/software/cryoem/relion/src/jaz/obs_model.cpp,
> line 688
> > > ERROR:
> > > ObservationModel::getBoxSize: box sizes not available.
> Make sure
> > > particle images are available before converting/importing
> STAR files
> > > from earlier versions of RELION.
> > >
> > > === Backtrace ===
> > >
> >
> /usr/local/relion/bin/relion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41)
> > > [0x434671]
> > >
> >
> /usr/local/relion/bin/relion_refine(_ZNK16ObservationModel10getBoxSizeEi+0x6b)
> >
> > > [0x4fcd0b]
> > >
> >
> /usr/local/relion/bin/relion_refine(_ZN7MlModel20initialiseFromImagesE8FileNamebR10ExperimentRbS3_S3_dbb+0xc9)
> >
> > > [0x60c499]
> > >
> >
> /usr/local/relion/bin/relion_refine(_ZN11MlOptimiser17initialiseGeneralEi+0x4ff)
> >
> > > [0x4827ef]
> > >
> >
> /usr/local/relion/bin/relion_refine(_ZN11MlOptimiser10initialiseEv+0x2f)
> >
> > > [0x48522f]
> > > /usr/local/relion/bin/relion_refine(main+0x33) [0x427bc3]
> > > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f6828084505]
> > > /usr/local/relion/bin/relion_refine() [0x42865f]
> > > ==================
> > > ERROR:
> > > ObservationModel::getBoxSize: box sizes not available.
> Make sure
> > > particle images are available before converting/importing
> STAR files
> > > from earlier versions of RELION.*
> > > *
> > > *
> > > What might went wrong,**
> > > *Best regards, *
> > > *E.R*
> > >
> > >
> >
> ------------------------------------------------------------------------
> > >
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> >
>
>
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