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From: Grigory S. <sha...@gm...> - 2021-09-27 12:02:38
|
I don't understand what you are trying to do :) The plugin v4.0b2 can work with both 3.1.2 and 4.0 Relion binaries. The 4.0 binaries are not provided by Scipion, you have to install them yourself. 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 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Sep 27, 2021 at 12:58 PM Dmitry Semchonok <Sem...@gm...> wrote: > Yes, it exists. > > I installed relion 3.1.2 via the plugin and currently it runs fine. > > > But there is still a riddle - how to run the relion 4.0b2? > > Sincerely, > Dmitry > > > On 27. Sep 2021, at 13:53, Grigory Sharov <sha...@gm...> > wrote: > > Thank you. You don't have to update as the new plugin should work with > relion 3. > > Does /home/user/Data/Software/scipion3/software/em/relion-3.1.2 exist? > > 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 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Mon, Sep 27, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm...> > wrote: > >> Dear Grigory, >> >> [user@dataanalysisserver1 ~]$ scipion3 config -p relion >> Scipion v3.0.9 - Eugenius >> Variables defined by plugin 'relion': >> >> RELION_HOME = /home/user/Data/Software/scipion3/software/em/relion-3.1.2 >> RELION_CUDA_LIB = /usr/local/cuda/lib64 >> RELION_PYTHON = None >> >> These variables can be added/edited in >> '/home/user/Data/Software/scipion3/config/scipion.conf’ >> >> >> >> >> So it seems to be 3.1.2. >> >> Shall I update for the 4.0 via the plugin command? >> >> Sincerely, >> Dmitry >> >> >> >> >> >> On 27. Sep 2021, at 13:47, Grigory Sharov <sha...@gm...> >> wrote: >> >> You can see the version via *scipion config -p relion* >> >> 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 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Mon, Sep 27, 2021 at 12:44 PM Dmitry Semchonok <Sem...@gm...> >> wrote: >> >>> Dear Grigory, >>> >>> Sorry, but how to verify the version? >>> >>> I the plugin I see scipion-em-relion >>> Relion-3.1.3 >>> >>> >>> Shall I also update for relion-4.0? >>> >>> Sincerely, >>> >>> Dmitry >>> >>> >>> >>> On 27. Sep 2021, at 13:40, Grigory Sharov <sha...@gm...> >>> wrote: >>> >>> Hi Dmitry, >>> >>> you are looking at a wrong tab, check run.stderr. Also, are you >>> running relion 3.1? >>> >>> 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 267228 <+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <Sem...@gm...> >>> wrote: >>> >>>> Dear Grigory & colleagues, >>>> >>>> Error running updated relion plugin. >>>> >>>> >>>> Any ideas? >>>> >>>> Thank you >>>> >>>> Sincerely, >>>> Dmitry >>>> >>>> >>>> >>>> >>>> File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't >>>> existFile 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't >>>> exist00001: Logging configured. STDOUT --> >>>> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> >>>> Runs/004970_ProtRelionClassify2D/logs/run.stderr >>>> 00002: RUNNING PROTOCOL ----------------- >>>> 00003: Protocol starts >>>> 00004: Hostname: localhost4.localdomain4 >>>> 00005: PID: 99422 >>>> 00006: pyworkflow: 3.0.17 >>>> 00007: plugin: relion >>>> 00008: plugin v: 4.0b2 >>>> 00009: currentDir: >>>> /home/user/Data/ScipionUserData/projects/Quentin__august__PSI >>>> 00010: workingDir: Runs/004970_ProtRelionClassify2D >>>> 00011: runMode: Continue >>>> 00012: MPI: 6 >>>> 00013: threads: 4 >>>> 00014: Starting at step: 1 >>>> 00015: Running steps >>>> 00016: STARTED: convertInputStep, step 1, time 2021-09-27 >>>> 13:14:18.891805 >>>> 00017: Converting set from >>>> 'Runs/001948_ProtUserSubSet/particles.sqlite' into >>>> 'Runs/004970_ProtRelionClassify2D/input_particles.star' >>>> 00018: convertBinaryFiles: creating soft links. >>>> 00019: Root: Runs/004970_ProtRelionClassify2D/extra/input -> >>>> Runs/001072_ProtRelionExtractParticles/extra >>>> 00020: FINISHED: convertInputStep, step 1, time 2021-09-27 >>>> 13:14:20.274397 >>>> 00021: STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078 >>>> 00022: mpirun -np 6 `which relion_refine_mpi` --i >>>> Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter >>>> 346 --ctf --zero_mask --K 24 --norm --scale --o >>>> Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 >>>> --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 >>>> --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 >>>> --gpu --j 4 >>>> 00023: Protocol failed: Command ' mpirun -np 6 `which >>>> relion_refine_mpi` --i >>>> Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter >>>> 346 --ctf --zero_mask --K 24 --norm --scale --o >>>> Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 >>>> --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 >>>> --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 >>>> --gpu --j 4' returned non-zero exit status 213. >>>> 00024: FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854 >>>> 00025: *** Last status is failed >>>> 00026: ------------------- PROTOCOL FAILED (DONE 2/3) >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Dmitry S. <Sem...@gm...> - 2021-09-27 11:58:16
|
Yes, it exists. I installed relion 3.1.2 via the plugin and currently it runs fine. But there is still a riddle - how to run the relion 4.0b2? Sincerely, Dmitry > On 27. Sep 2021, at 13:53, Grigory Sharov <sha...@gm...> wrote: > > Thank you. You don't have to update as the new plugin should work with relion 3. > > Does /home/user/Data/Software/scipion3/software/em/relion-3.1.2 exist? > > 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 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Mon, Sep 27, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > Dear Grigory, > > [user@dataanalysisserver1 ~]$ scipion3 config -p relion > Scipion v3.0.9 - Eugenius > Variables defined by plugin 'relion': > > RELION_HOME = /home/user/Data/Software/scipion3/software/em/relion-3.1.2 > RELION_CUDA_LIB = /usr/local/cuda/lib64 > RELION_PYTHON = None > > These variables can be added/edited in '/home/user/Data/Software/scipion3/config/scipion.conf’ > > > > > So it seems to be 3.1.2. > > Shall I update for the 4.0 via the plugin command? > > Sincerely, > Dmitry > > > > > >> On 27. Sep 2021, at 13:47, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >> >> You can see the version via scipion config -p relion >> >> 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 267228 <tel:+44%201223%20267228> >> e-mail: gs...@mr... <mailto:gs...@mr...> >> >> >> On Mon, Sep 27, 2021 at 12:44 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >> Dear Grigory, >> >> Sorry, but how to verify the version? >> >> I the plugin I see scipion-em-relion >> Relion-3.1.3 >> >> >> Shall I also update for relion-4.0? >> >> Sincerely, >> >> Dmitry >> >> >> >>> On 27. Sep 2021, at 13:40, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >>> >>> Hi Dmitry, >>> >>> you are looking at a wrong tab, check run.stderr. Also, are you running relion 3.1? >>> >>> 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 267228 <tel:+44%201223%20267228> >>> e-mail: gs...@mr... <mailto:gs...@mr...> >>> >>> >>> On Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>> Dear Grigory & colleagues, >>> >>> Error running updated relion plugin. >>> >>> >>> Any ideas? >>> >>> Thank you >>> >>> Sincerely, >>> Dmitry >>> >>> >>> >>> >>> File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't existFile 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't exist00001: Logging configured. STDOUT --> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> Runs/004970_ProtRelionClassify2D/logs/run.stderr >>> 00002: RUNNING PROTOCOL ----------------- >>> 00003: Protocol starts >>> 00004: Hostname: localhost4.localdomain4 >>> 00005: PID: 99422 >>> 00006: pyworkflow: 3.0.17 >>> 00007: plugin: relion >>> 00008: plugin v: 4.0b2 >>> 00009: currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI >>> 00010: workingDir: Runs/004970_ProtRelionClassify2D >>> 00011: runMode: Continue >>> 00012: MPI: 6 >>> 00013: threads: 4 >>> 00014: Starting at step: 1 >>> 00015: Running steps >>> 00016: STARTED: convertInputStep, step 1, time 2021-09-27 13:14:18.891805 >>> 00017: Converting set from 'Runs/001948_ProtUserSubSet/particles.sqlite' into 'Runs/004970_ProtRelionClassify2D/input_particles.star' >>> 00018: convertBinaryFiles: creating soft links. >>> 00019: Root: Runs/004970_ProtRelionClassify2D/extra/input -> Runs/001072_ProtRelionExtractParticles/extra >>> 00020: FINISHED: convertInputStep, step 1, time 2021-09-27 13:14:20.274397 >>> 00021: STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078 >>> 00022: mpirun -np 6 `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf --zero_mask --K 24 --norm --scale --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 --gpu --j 4 >>> 00023: Protocol failed: Command ' mpirun -np 6 `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf --zero_mask --K 24 --norm --scale --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 --gpu --j 4' returned non-zero exit status 213. >>> 00024: FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854 >>> 00025: *** Last status is failed >>> 00026: ------------------- PROTOCOL FAILED (DONE 2/3) >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
|
From: Grigory S. <sha...@gm...> - 2021-09-27 11:53:52
|
Thank you. You don't have to update as the new plugin should work with relion 3. Does /home/user/Data/Software/scipion3/software/em/relion-3.1.2 exist? 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 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Sep 27, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear Grigory, > > [user@dataanalysisserver1 ~]$ scipion3 config -p relion > Scipion v3.0.9 - Eugenius > Variables defined by plugin 'relion': > > RELION_HOME = /home/user/Data/Software/scipion3/software/em/relion-3.1.2 > RELION_CUDA_LIB = /usr/local/cuda/lib64 > RELION_PYTHON = None > > These variables can be added/edited in > '/home/user/Data/Software/scipion3/config/scipion.conf’ > > > > > So it seems to be 3.1.2. > > Shall I update for the 4.0 via the plugin command? > > Sincerely, > Dmitry > > > > > > On 27. Sep 2021, at 13:47, Grigory Sharov <sha...@gm...> > wrote: > > You can see the version via *scipion config -p relion* > > 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 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Mon, Sep 27, 2021 at 12:44 PM Dmitry Semchonok <Sem...@gm...> > wrote: > >> Dear Grigory, >> >> Sorry, but how to verify the version? >> >> I the plugin I see scipion-em-relion >> Relion-3.1.3 >> >> >> Shall I also update for relion-4.0? >> >> Sincerely, >> >> Dmitry >> >> >> >> On 27. Sep 2021, at 13:40, Grigory Sharov <sha...@gm...> >> wrote: >> >> Hi Dmitry, >> >> you are looking at a wrong tab, check run.stderr. Also, are you >> running relion 3.1? >> >> 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 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <Sem...@gm...> >> wrote: >> >>> Dear Grigory & colleagues, >>> >>> Error running updated relion plugin. >>> >>> >>> Any ideas? >>> >>> Thank you >>> >>> Sincerely, >>> Dmitry >>> >>> >>> >>> >>> File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't >>> existFile 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't >>> exist00001: Logging configured. STDOUT --> >>> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> >>> Runs/004970_ProtRelionClassify2D/logs/run.stderr >>> 00002: RUNNING PROTOCOL ----------------- >>> 00003: Protocol starts >>> 00004: Hostname: localhost4.localdomain4 >>> 00005: PID: 99422 >>> 00006: pyworkflow: 3.0.17 >>> 00007: plugin: relion >>> 00008: plugin v: 4.0b2 >>> 00009: currentDir: >>> /home/user/Data/ScipionUserData/projects/Quentin__august__PSI >>> 00010: workingDir: Runs/004970_ProtRelionClassify2D >>> 00011: runMode: Continue >>> 00012: MPI: 6 >>> 00013: threads: 4 >>> 00014: Starting at step: 1 >>> 00015: Running steps >>> 00016: STARTED: convertInputStep, step 1, time 2021-09-27 >>> 13:14:18.891805 >>> 00017: Converting set from >>> 'Runs/001948_ProtUserSubSet/particles.sqlite' into >>> 'Runs/004970_ProtRelionClassify2D/input_particles.star' >>> 00018: convertBinaryFiles: creating soft links. >>> 00019: Root: Runs/004970_ProtRelionClassify2D/extra/input -> >>> Runs/001072_ProtRelionExtractParticles/extra >>> 00020: FINISHED: convertInputStep, step 1, time 2021-09-27 >>> 13:14:20.274397 >>> 00021: STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078 >>> 00022: mpirun -np 6 `which relion_refine_mpi` --i >>> Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter >>> 346 --ctf --zero_mask --K 24 --norm --scale --o >>> Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 >>> --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 >>> --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 >>> --gpu --j 4 >>> 00023: Protocol failed: Command ' mpirun -np 6 `which >>> relion_refine_mpi` --i >>> Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter >>> 346 --ctf --zero_mask --K 24 --norm --scale --o >>> Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 >>> --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 >>> --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 >>> --gpu --j 4' returned non-zero exit status 213. >>> 00024: FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854 >>> 00025: *** Last status is failed >>> 00026: ------------------- PROTOCOL FAILED (DONE 2/3) >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <Sem...@gm...> - 2021-09-27 11:51:04
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Dear Grigory, [user@dataanalysisserver1 ~]$ scipion3 config -p relion Scipion v3.0.9 - Eugenius Variables defined by plugin 'relion': RELION_HOME = /home/user/Data/Software/scipion3/software/em/relion-3.1.2 RELION_CUDA_LIB = /usr/local/cuda/lib64 RELION_PYTHON = None These variables can be added/edited in '/home/user/Data/Software/scipion3/config/scipion.conf’ So it seems to be 3.1.2. Shall I update for the 4.0 via the plugin command? Sincerely, Dmitry > On 27. Sep 2021, at 13:47, Grigory Sharov <sha...@gm...> wrote: > > You can see the version via scipion config -p relion > > 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 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Mon, Sep 27, 2021 at 12:44 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > Dear Grigory, > > Sorry, but how to verify the version? > > I the plugin I see scipion-em-relion > Relion-3.1.3 > > > Shall I also update for relion-4.0? > > Sincerely, > > Dmitry > > > >> On 27. Sep 2021, at 13:40, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >> >> Hi Dmitry, >> >> you are looking at a wrong tab, check run.stderr. Also, are you running relion 3.1? >> >> 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 267228 <tel:+44%201223%20267228> >> e-mail: gs...@mr... <mailto:gs...@mr...> >> >> >> On Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >> Dear Grigory & colleagues, >> >> Error running updated relion plugin. >> >> >> Any ideas? >> >> Thank you >> >> Sincerely, >> Dmitry >> >> >> >> >> File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't existFile 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't exist00001: Logging configured. STDOUT --> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> Runs/004970_ProtRelionClassify2D/logs/run.stderr >> 00002: RUNNING PROTOCOL ----------------- >> 00003: Protocol starts >> 00004: Hostname: localhost4.localdomain4 >> 00005: PID: 99422 >> 00006: pyworkflow: 3.0.17 >> 00007: plugin: relion >> 00008: plugin v: 4.0b2 >> 00009: currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI >> 00010: workingDir: Runs/004970_ProtRelionClassify2D >> 00011: runMode: Continue >> 00012: MPI: 6 >> 00013: threads: 4 >> 00014: Starting at step: 1 >> 00015: Running steps >> 00016: STARTED: convertInputStep, step 1, time 2021-09-27 13:14:18.891805 >> 00017: Converting set from 'Runs/001948_ProtUserSubSet/particles.sqlite' into 'Runs/004970_ProtRelionClassify2D/input_particles.star' >> 00018: convertBinaryFiles: creating soft links. >> 00019: Root: Runs/004970_ProtRelionClassify2D/extra/input -> Runs/001072_ProtRelionExtractParticles/extra >> 00020: FINISHED: convertInputStep, step 1, time 2021-09-27 13:14:20.274397 >> 00021: STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078 >> 00022: mpirun -np 6 `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf --zero_mask --K 24 --norm --scale --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 --gpu --j 4 >> 00023: Protocol failed: Command ' mpirun -np 6 `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf --zero_mask --K 24 --norm --scale --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 --gpu --j 4' returned non-zero exit status 213. >> 00024: FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854 >> 00025: *** Last status is failed >> 00026: ------------------- PROTOCOL FAILED (DONE 2/3) >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-27 11:47:44
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You can see the version via *scipion config -p relion* 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 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Sep 27, 2021 at 12:44 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear Grigory, > > Sorry, but how to verify the version? > > I the plugin I see scipion-em-relion > Relion-3.1.3 > > > Shall I also update for relion-4.0? > > Sincerely, > > Dmitry > > > > On 27. Sep 2021, at 13:40, Grigory Sharov <sha...@gm...> > wrote: > > Hi Dmitry, > > you are looking at a wrong tab, check run.stderr. Also, are you > running relion 3.1? > > 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 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <Sem...@gm...> > wrote: > >> Dear Grigory & colleagues, >> >> Error running updated relion plugin. >> >> >> Any ideas? >> >> Thank you >> >> Sincerely, >> Dmitry >> >> >> >> >> File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't existFile >> 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't exist00001: >> Logging configured. STDOUT --> >> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> >> Runs/004970_ProtRelionClassify2D/logs/run.stderr >> 00002: RUNNING PROTOCOL ----------------- >> 00003: Protocol starts >> 00004: Hostname: localhost4.localdomain4 >> 00005: PID: 99422 >> 00006: pyworkflow: 3.0.17 >> 00007: plugin: relion >> 00008: plugin v: 4.0b2 >> 00009: currentDir: >> /home/user/Data/ScipionUserData/projects/Quentin__august__PSI >> 00010: workingDir: Runs/004970_ProtRelionClassify2D >> 00011: runMode: Continue >> 00012: MPI: 6 >> 00013: threads: 4 >> 00014: Starting at step: 1 >> 00015: Running steps >> 00016: STARTED: convertInputStep, step 1, time 2021-09-27 >> 13:14:18.891805 >> 00017: Converting set from >> 'Runs/001948_ProtUserSubSet/particles.sqlite' into >> 'Runs/004970_ProtRelionClassify2D/input_particles.star' >> 00018: convertBinaryFiles: creating soft links. >> 00019: Root: Runs/004970_ProtRelionClassify2D/extra/input -> >> Runs/001072_ProtRelionExtractParticles/extra >> 00020: FINISHED: convertInputStep, step 1, time 2021-09-27 >> 13:14:20.274397 >> 00021: STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078 >> 00022: mpirun -np 6 `which relion_refine_mpi` --i >> Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter >> 346 --ctf --zero_mask --K 24 --norm --scale --o >> Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 >> --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 >> --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 >> --gpu --j 4 >> 00023: Protocol failed: Command ' mpirun -np 6 `which >> relion_refine_mpi` --i >> Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter >> 346 --ctf --zero_mask --K 24 --norm --scale --o >> Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 >> --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 >> --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 >> --gpu --j 4' returned non-zero exit status 213. >> 00024: FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854 >> 00025: *** Last status is failed >> 00026: ------------------- PROTOCOL FAILED (DONE 2/3) > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <Sem...@gm...> - 2021-09-27 11:44:28
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Dear Grigory, Sorry, but how to verify the version? I the plugin I see scipion-em-relion Relion-3.1.3 Shall I also update for relion-4.0? Sincerely, Dmitry > On 27. Sep 2021, at 13:40, Grigory Sharov <sha...@gm...> wrote: > > Hi Dmitry, > > you are looking at a wrong tab, check run.stderr. Also, are you running relion 3.1? > > 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 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > Dear Grigory & colleagues, > > Error running updated relion plugin. > > > Any ideas? > > Thank you > > Sincerely, > Dmitry > > > > > File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't existFile 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't exist00001: Logging configured. STDOUT --> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> Runs/004970_ProtRelionClassify2D/logs/run.stderr > 00002: RUNNING PROTOCOL ----------------- > 00003: Protocol starts > 00004: Hostname: localhost4.localdomain4 > 00005: PID: 99422 > 00006: pyworkflow: 3.0.17 > 00007: plugin: relion > 00008: plugin v: 4.0b2 > 00009: currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI > 00010: workingDir: Runs/004970_ProtRelionClassify2D > 00011: runMode: Continue > 00012: MPI: 6 > 00013: threads: 4 > 00014: Starting at step: 1 > 00015: Running steps > 00016: STARTED: convertInputStep, step 1, time 2021-09-27 13:14:18.891805 > 00017: Converting set from 'Runs/001948_ProtUserSubSet/particles.sqlite' into 'Runs/004970_ProtRelionClassify2D/input_particles.star' > 00018: convertBinaryFiles: creating soft links. > 00019: Root: Runs/004970_ProtRelionClassify2D/extra/input -> Runs/001072_ProtRelionExtractParticles/extra > 00020: FINISHED: convertInputStep, step 1, time 2021-09-27 13:14:20.274397 > 00021: STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078 > 00022: mpirun -np 6 `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf --zero_mask --K 24 --norm --scale --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 --gpu --j 4 > 00023: Protocol failed: Command ' mpirun -np 6 `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf --zero_mask --K 24 --norm --scale --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 --gpu --j 4' returned non-zero exit status 213. > 00024: FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854 > 00025: *** Last status is failed > 00026: ------------------- PROTOCOL FAILED (DONE 2/3) > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-27 11:40:46
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Hi Dmitry, you are looking at a wrong tab, check run.stderr. Also, are you running relion 3.1? 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 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <Sem...@gm...> wrote: > Dear Grigory & colleagues, > > Error running updated relion plugin. > > > Any ideas? > > Thank you > > Sincerely, > Dmitry > > > > > File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't existFile > 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't exist00001: > Logging configured. STDOUT --> > Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> > Runs/004970_ProtRelionClassify2D/logs/run.stderr > 00002: RUNNING PROTOCOL ----------------- > 00003: Protocol starts > 00004: Hostname: localhost4.localdomain4 > 00005: PID: 99422 > 00006: pyworkflow: 3.0.17 > 00007: plugin: relion > 00008: plugin v: 4.0b2 > 00009: currentDir: > /home/user/Data/ScipionUserData/projects/Quentin__august__PSI > 00010: workingDir: Runs/004970_ProtRelionClassify2D > 00011: runMode: Continue > 00012: MPI: 6 > 00013: threads: 4 > 00014: Starting at step: 1 > 00015: Running steps > 00016: STARTED: convertInputStep, step 1, time 2021-09-27 13:14:18.891805 > 00017: Converting set from 'Runs/001948_ProtUserSubSet/particles.sqlite' > into 'Runs/004970_ProtRelionClassify2D/input_particles.star' > 00018: convertBinaryFiles: creating soft links. > 00019: Root: Runs/004970_ProtRelionClassify2D/extra/input -> > Runs/001072_ProtRelionExtractParticles/extra > 00020: FINISHED: convertInputStep, step 1, time 2021-09-27 > 13:14:20.274397 > 00021: STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078 > 00022: mpirun -np 6 `which relion_refine_mpi` --i > Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter > 346 --ctf --zero_mask --K 24 --norm --scale --o > Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 > --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 > --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 > --gpu --j 4 > 00023: Protocol failed: Command ' mpirun -np 6 `which > relion_refine_mpi` --i > Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter > 346 --ctf --zero_mask --K 24 --norm --scale --o > Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 > --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 > --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 > --gpu --j 4' returned non-zero exit status 213. > 00024: FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854 > 00025: *** Last status is failed > 00026: ------------------- PROTOCOL FAILED (DONE 2/3) |
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From: Dmitry S. <Sem...@gm...> - 2021-09-27 11:18:53
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Dear Grigory & colleagues, Error running updated relion plugin. Any ideas? Thank you Sincerely, Dmitry File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't existFile 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't exist00001: Logging configured. STDOUT --> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> Runs/004970_ProtRelionClassify2D/logs/run.stderr 00002: RUNNING PROTOCOL ----------------- 00003: Protocol starts 00004: Hostname: localhost4.localdomain4 00005: PID: 99422 00006: pyworkflow: 3.0.17 00007: plugin: relion 00008: plugin v: 4.0b2 00009: currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI 00010: workingDir: Runs/004970_ProtRelionClassify2D 00011: runMode: Continue 00012: MPI: 6 00013: threads: 4 00014: Starting at step: 1 00015: Running steps 00016: STARTED: convertInputStep, step 1, time 2021-09-27 13:14:18.891805 00017: Converting set from 'Runs/001948_ProtUserSubSet/particles.sqlite' into 'Runs/004970_ProtRelionClassify2D/input_particles.star' 00018: convertBinaryFiles: creating soft links. 00019: Root: Runs/004970_ProtRelionClassify2D/extra/input -> Runs/001072_ProtRelionExtractParticles/extra 00020: FINISHED: convertInputStep, step 1, time 2021-09-27 13:14:20.274397 00021: STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078 00022: mpirun -np 6 `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf --zero_mask --K 24 --norm --scale --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 --gpu --j 4 00023: Protocol failed: Command ' mpirun -np 6 `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf --zero_mask --K 24 --norm --scale --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 --gpu --j 4' returned non-zero exit status 213. 00024: FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854 00025: *** Last status is failed 00026: ------------------- PROTOCOL FAILED (DONE 2/3) |
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From: Grigory S. <sha...@gm...> - 2021-09-27 09:55:31
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I found my mistake. The following will fix it (wait a few minutes, the release is building on pypi now): *scipion installp -p scipion-em-relion 4.0b2 --noBin* Thank you for reporting it, Dmitry! 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 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Sep 27, 2021 at 10:30 AM Dmitry Semchonok <Sem...@gm...> wrote: > I removed the relion plugin completely and then install as it was in the > email — *scipion installp -p scipion-em-relion 4.0b1 --noBin. *(in my > case scipion3 installp -p scipion-em-relion 4.0b1 --noBin) --- the result > is the same [image: :slightly_smiling_face:] > > > Sincerely, > > Dmitry > > > On 27. Sep 2021, at 11:25, Grigory Sharov <sha...@gm...> > wrote: > > Hi Dmitry, > > Have you tried to update scipion (scipion update?)? > I don't use plugin manager much, so I suggest running plugin update via > cmdline as in the email. > > 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 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Mon, Sep 27, 2021 at 10:16 AM Dmitry Semchonok <Sem...@gm...> > wrote: > >> Dear Grigory & colleagues, >> >> After update the relion plugin via plugin manager the relion disappeared >> from the list of the plugins instead I have the following error >> >> >> >> Scipion v3.0.9 - Eugenius >> > error when importing from relion.protocols: No module named >> 'relion.protocols._legacy' >> File >> "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/__init__.py", >> line 61, in <module> >> Check the plugin manager (Configuration->Plugins in Scipion manager >> window) >> or use 'scipion installp --help --checkUpdates' in the command line to >> check for upgrades, >> it could be a versions compatibility issue. >> >> >> >> >> Any solution? >> >> Thank you >> >> Sincerely, >> Dmitry >> >> >> >> >> >> >> >> _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Dmitry S. <Sem...@gm...> - 2021-09-27 09:36:50
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Dear Grigory & colleagues, After update the relion plugin via plugin manager the relion disappeared from the list of the plugins instead I have the following error Scipion v3.0.9 - Eugenius > error when importing from relion.protocols: No module named 'relion.protocols._legacy' File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/__init__.py", line 61, in <module> Check the plugin manager (Configuration->Plugins in Scipion manager window) or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, it could be a versions compatibility issue. Any solution? Thank you Sincerely, Dmitry |
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From: Dmitry S. <Sem...@gm...> - 2021-09-27 09:29:52
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I removed the relion plugin completely and then install as it was in the email — scipion installp -p scipion-em-relion 4.0b1 --noBin. (in my case scipion3 installp -p scipion-em-relion 4.0b1 --noBin) --- the result is the same Sincerely, Dmitry > On 27. Sep 2021, at 11:25, Grigory Sharov <sha...@gm...> wrote: > > Hi Dmitry, > > Have you tried to update scipion (scipion update?)? > I don't use plugin manager much, so I suggest running plugin update via cmdline as in the email. > > 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 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Mon, Sep 27, 2021 at 10:16 AM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > Dear Grigory & colleagues, > > After update the relion plugin via plugin manager the relion disappeared from the list of the plugins instead I have the following error > > > > Scipion v3.0.9 - Eugenius > > error when importing from relion.protocols: No module named 'relion.protocols._legacy' > File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/__init__.py", line 61, in <module> > Check the plugin manager (Configuration->Plugins in Scipion manager window) > or use 'scipion installp --help --checkUpdates' in the command line to check for upgrades, > it could be a versions compatibility issue. > > > > > Any solution? > > Thank you > > Sincerely, > Dmitry > > > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-27 09:25:44
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Hi Dmitry, Have you tried to update scipion (scipion update?)? I don't use plugin manager much, so I suggest running plugin update via cmdline as in the email. 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 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Sep 27, 2021 at 10:16 AM Dmitry Semchonok <Sem...@gm...> wrote: > Dear Grigory & colleagues, > > After update the relion plugin via plugin manager the relion disappeared > from the list of the plugins instead I have the following error > > > > Scipion v3.0.9 - Eugenius > > error when importing from relion.protocols: No module named > 'relion.protocols._legacy' > File > "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/relion/protocols/__init__.py", > line 61, in <module> > Check the plugin manager (Configuration->Plugins in Scipion manager > window) > or use 'scipion installp --help --checkUpdates' in the command line to > check for upgrades, > it could be a versions compatibility issue. > > > > > Any solution? > > Thank you > > Sincerely, > Dmitry > > > > > > > > |
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From: Pablo C. <pc...@cn...> - 2021-09-27 08:49:57
|
Excellent news, Grigory! On 25/9/21 18:53, Grigory Sharov wrote: > Dear all, > > those of you who would like to try Relion 4 with Scipion can install > the latest plugin version and create a link to relion-4.0 in > software/em (installation via scipion is not available): > > *scipion installp -p scipion-em-relion 4.0b1 --noBin* > > More detailed changes are: > > * new 2D class ranker protocol > * new env var RELION_PYTHON for Python with Torch & Numpy modules > (required for the protocol above) > * float16 option added but disabled since xmipp does not support > that format > * EER support enabled (only upsampling 1x is recommended and tested) > * 3.1.3 binary added > * BUGFIX: wrong shifts were saved in motioncor when skipping frames > * Multi-body protocol improvements, viewer added > * Postprocessing now supports multi-body input > > > As this is a beta version of the plugin, you could expect some bugs. > Let us know if you encounter any issues. > > 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 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
|
From: Grigory S. <sha...@gm...> - 2021-09-25 18:11:01
|
Hello Roberto, Yes, relion 3.1 should be fine with the new plugin. Let me know if something is broken On Sat, Sep 25, 2021, 18:49 Roberto Marabini <ro...@cn...> wrote: > Thanks Grigory ;-). In case I do not like relion 4, will I be able to use > RElion 3.X from this version of the plugin? > > cheers > > Roberto > > > On Sat, Sep 25, 2021 at 6:53 PM Grigory Sharov <sha...@gm...> > wrote: > >> Dear all, >> >> those of you who would like to try Relion 4 with Scipion can install the >> latest plugin version and create a link to relion-4.0 in software/em >> (installation via scipion is not available): >> >> *scipion installp -p scipion-em-relion 4.0b1 --noBin* >> >> More detailed changes are: >> >> >> - new 2D class ranker protocol >> - new env var RELION_PYTHON for Python with Torch & Numpy modules >> (required for the protocol above) >> - float16 option added but disabled since xmipp does not support that >> format >> - EER support enabled (only upsampling 1x is recommended and tested) >> - 3.1.3 binary added >> - BUGFIX: wrong shifts were saved in motioncor when skipping frames >> - Multi-body protocol improvements, viewer added >> - Postprocessing now supports multi-body input >> >> >> As this is a beta version of the plugin, you could expect some bugs. Let >> us know if you encounter any issues. >> >> 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 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Roberto M. <ro...@cn...> - 2021-09-25 17:49:42
|
Thanks Grigory ;-). In case I do not like relion 4, will I be able to use
RElion 3.X from this version of the plugin?
cheers
Roberto
On Sat, Sep 25, 2021 at 6:53 PM Grigory Sharov <sha...@gm...>
wrote:
> Dear all,
>
> those of you who would like to try Relion 4 with Scipion can install the
> latest plugin version and create a link to relion-4.0 in software/em
> (installation via scipion is not available):
>
> *scipion installp -p scipion-em-relion 4.0b1 --noBin*
>
> More detailed changes are:
>
>
> - new 2D class ranker protocol
> - new env var RELION_PYTHON for Python with Torch & Numpy modules
> (required for the protocol above)
> - float16 option added but disabled since xmipp does not support that
> format
> - EER support enabled (only upsampling 1x is recommended and tested)
> - 3.1.3 binary added
> - BUGFIX: wrong shifts were saved in motioncor when skipping frames
> - Multi-body protocol improvements, viewer added
> - Postprocessing now supports multi-body input
>
>
> As this is a beta version of the plugin, you could expect some bugs. Let
> us know if you encounter any issues.
>
> 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 267228 <+44%201223%20267228>
> e-mail: gs...@mr...
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Grigory S. <sha...@gm...> - 2021-09-25 16:53:34
|
Dear all, those of you who would like to try Relion 4 with Scipion can install the latest plugin version and create a link to relion-4.0 in software/em (installation via scipion is not available): *scipion installp -p scipion-em-relion 4.0b1 --noBin* More detailed changes are: - new 2D class ranker protocol - new env var RELION_PYTHON for Python with Torch & Numpy modules (required for the protocol above) - float16 option added but disabled since xmipp does not support that format - EER support enabled (only upsampling 1x is recommended and tested) - 3.1.3 binary added - BUGFIX: wrong shifts were saved in motioncor when skipping frames - Multi-body protocol improvements, viewer added - Postprocessing now supports multi-body input As this is a beta version of the plugin, you could expect some bugs. Let us know if you encounter any issues. 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 267228 <+44%201223%20267228> e-mail: gs...@mr... |
|
From: Grigory S. <sha...@gm...> - 2021-09-24 13:58:32
|
Hi Emil, this is not implemented. You have to run relion motioncor within Scipion and then get power spectra that can be used by cistem - ctffind protocol 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 267228 <+44%201223%20267228> e-mail: gs...@mr... On Fri, Sep 24, 2021 at 2:44 PM Emil Tykesson <emi...@me...> wrote: > Hi! > > I am trying to import motion corrected micrographs from Relion, but can > not seem to succeed in also importing their associated power spectra. Since > they are created as two separate mrc files in Relion I am not sure how to > parse both into Scipion. Can you please advise? > > Best wishes, > Emil > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Emil T. <emi...@me...> - 2021-09-24 13:05:17
|
Hi! I am trying to import motion corrected micrographs from Relion, but can not seem to succeed in also importing their associated power spectra. Since they are created as two separate mrc files in Relion I am not sure how to parse both into Scipion. Can you please advise? Best wishes, Emil |
|
From: Genís V. G. <gen...@ki...> - 2021-09-21 14:49:20
|
Hi Grigory Many thanks, worked like a charm! Genis Genis Valentin Gese | Postdoctoral researcher Martin Hällberg group Cell and Molecular Biology Department | Karolinska Institutet 171 65 Stockholm | Solnavägen 9 gen...@ki...<mailto:fir...@ki...> | ki.se<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fki.se%2Fen%2Fstartpage&data=02%7C01%7Cgenis.valentin.gese%40ki.se%7C96f824255829424948f308d82a5e4ec9%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637305931833981292&sdata=yXbUoiFkJqjlBIYtLNaNEXIlydBY8N0LVZ5C9bWR5nU%3D&reserved=0> ________________________________ Från: Grigory Sharov <sha...@gm...> Skickat: den 21 september 2021 14:52 Till: Mailing list for Scipion users <sci...@li...> Ämne: Re: [scipion-users] Relion re-group particles Hi Genis, Sure, you can do this on the CTF tab of a relion protocol as shown below. Only grouping by defocus is implemented. [Screenshot_20210921_135024.png] 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 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Mon, Sep 20, 2021 at 10:23 PM Genís Valentín Gesé <gen...@ki...<mailto:gen...@ki...>> wrote: Hi everyone! When running relion jobs, I get many warnings similar to this one: WARNING: There are only 3 particles in group 6 of half-set 1 In the relion GUI this can be fixed by re-grouping particles from the "Select" job. Is there a way to regroup particles within Scipion? Thanks and best regards! Genis Valentin Gese | Postdoctoral researcher Martin Hällberg group Cell and Molecular Biology Department | Karolinska Institutet 171 65 Stockholm | Solnavägen 9 gen...@ki...<mailto:fir...@ki...> | ki.se<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fki.se%2Fen%2Fstartpage&data=04%7C01%7Cgenis.valentin.gese%40ki.se%7Cacec253d3b304ac78e2708d97cfee86e%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637678256537755293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=1PecBCrYzaMlLmbo2TaLi5VM4v%2Fo1VP9P2%2Bkzhp3jOM%3D&reserved=0> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fki.se%2Fmedarbetare%2Fintegritetsskyddspolicy&data=04%7C01%7Cgenis.valentin.gese%40ki.se%7Cacec253d3b304ac78e2708d97cfee86e%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637678256537765243%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=HQOlzE1mVOay4iyS3wQ4lg0W8Iwbt7WMMxZHAA1iKhQ%3D&reserved=0>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>. _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cgenis.valentin.gese%40ki.se%7Cacec253d3b304ac78e2708d97cfee86e%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637678256537765243%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=AN0TmnmEpjGhJDBL9AeF5lMKBGfYMsBEDmTRhL9WV5A%3D&reserved=0> |
|
From: Grigory S. <sha...@gm...> - 2021-09-21 12:53:08
|
Hi Genis, Sure, you can do this on the CTF tab of a relion protocol as shown below. Only grouping by defocus is implemented. [image: Screenshot_20210921_135024.png] 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 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Sep 20, 2021 at 10:23 PM Genís Valentín Gesé < gen...@ki...> wrote: > Hi everyone! > > When running relion jobs, I get many warnings similar to this one: > WARNING: There are only 3 particles in group 6 of half-set 1 > > In the relion GUI this can be fixed by re-grouping particles from the > "Select" job. Is there a way to regroup particles within Scipion? > > Thanks and best regards! > > > *Genis Valentin Gese* | Postdoctoral researcher > > Martin Hällberg group > Cell and Molecular Biology Department | Karolinska Institutet > 171 65 Stockholm | Solnavägen 9 > gen...@ki... <fir...@ki...> | ki.se > <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fki.se%2Fen%2Fstartpage&data=02%7C01%7Cgenis.valentin.gese%40ki.se%7C96f824255829424948f308d82a5e4ec9%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637305931833981292&sdata=yXbUoiFkJqjlBIYtLNaNEXIlydBY8N0LVZ5C9bWR5nU%3D&reserved=0> > > > > *När du skickar e-post till Karolinska Institutet (KI) innebär detta att > KI kommer att behandla dina personuppgifter. *Här finns information om > hur KI behandlar personuppgifter > <https://ki.se/medarbetare/integritetsskyddspolicy>. > > > *Sending email to Karolinska Institutet (KI) will result in KI processing > your personal data.* You can read more about KI’s processing of personal > data here <https://ki.se/en/staff/data-protection-policy>. > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Genís V. G. <gen...@ki...> - 2021-09-20 21:23:13
|
Hi everyone! When running relion jobs, I get many warnings similar to this one: WARNING: There are only 3 particles in group 6 of half-set 1 In the relion GUI this can be fixed by re-grouping particles from the "Select" job. Is there a way to regroup particles within Scipion? Thanks and best regards! Genis Valentin Gese | Postdoctoral researcher Martin Hällberg group Cell and Molecular Biology Department | Karolinska Institutet 171 65 Stockholm | Solnavägen 9 gen...@ki...<mailto:fir...@ki...> | ki.se<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fki.se%2Fen%2Fstartpage&data=02%7C01%7Cgenis.valentin.gese%40ki.se%7C96f824255829424948f308d82a5e4ec9%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637305931833981292&sdata=yXbUoiFkJqjlBIYtLNaNEXIlydBY8N0LVZ5C9bWR5nU%3D&reserved=0> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://ki.se/en/staff/data-protection-policy>. |
|
From: Grigory S. <sha...@gm...> - 2021-09-20 21:02:31
|
Hi, Have you tried importing it as particles? 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 267228 <+44%201223%20267228> e-mail: gs...@mr... On Mon, Sep 20, 2021 at 9:59 PM Deniston, Colin <col...@no...> wrote: > Hi, > > > > I am running the goCTF software which will help assign per-particle CTF > info for particles in tilted images. I end up with a typical relion star > file with particle coordinates and individual defocus values for each > particle. How can I import this back into Scipion? If I import it as a > coordinate file it loses all the CTF info and I can’t figure out how to > import it as a CTF. Any guidance would be appreciated! > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Deniston, C. <col...@no...> - 2021-09-20 20:59:27
|
Hi, I am running the goCTF software which will help assign per-particle CTF info for particles in tilted images. I end up with a typical relion star file with particle coordinates and individual defocus values for each particle. How can I import this back into Scipion? If I import it as a coordinate file it loses all the CTF info and I can't figure out how to import it as a CTF. Any guidance would be appreciated! |
|
From: Pablo C. <pc...@cn...> - 2021-09-15 13:58:23
|
Hi Wolfgang!
You are right, in those cases you are going to need to import the half
maps individually to be chosen later on. (something to correct in the
future, or at least, leave as an "advance option".
Cheers!
On 15/9/21 14:16, Lugmayr, Wolfgang wrote:
> Hi Pablo,
>
> thank you and no worries, I prefer the solution part of your answers ;-)
>
> I just wanted for curiosity compare the results of fsc3d, bsoft
> blocres and resmap.
> the later two accept only real half-maps in their form.
>
> I will try.
>
> Cheers,
> Wolfgang
>
>
> ------------------------------------------------------------------------
> *From: *"Pablo Conesa" <pc...@cn...>
> *To: *"Mailing list for Scipion users"
> <sci...@li...>
> *Sent: *Wednesday, 15 September, 2021 11:12:11
> *Subject: *Re: [scipion-users] import volumes with half maps question
>
> Forgot a "Hi Wolfgang!" or something similar. Now reading it looks
> rude. Extremely far from my intention and mood ;-) . Happy em processing!
>
>
> On 15/9/21 10:53, Pablo Conesa wrote:
>
> Halves imported as halves will never be seen by the spyglass. The
> "main" volume will have the two halves associated "internally" and
> protocols in need of the halves will seek for this internal
> structure. Therefore providing the "main" volume will provide, at
> the same time the internal halves associated.
>
> Now, if you want to treat any half as a volume to be chosen from
> any spyglass button, then you need to import it as a "main" map.
>
> There might be a case where a protocol does not "expect" halves to
> be associated to a volume. Only in this case you'll need to import
> halves as main volumes. But we try to prevent this to reduce
> number of clicks and improve clarity as usability.
>
> Cheers!
>
> On 15/9/21 9:31, Lugmayr, Wolfgang wrote:
>
> Hi Marta,
>
> yes it worked, I did not expect to enter a file when the UI says "Files directory".
> Instead I tried to enter the file somehow in the "Pattern" input field.
> Maybe the help hints can be extended?
>
> Do I understand your description about half-maps attributes correctly?
> When I need to select 2 half-maps for e.g. ResMap FSC, I have to import them from the Relion job as single imports?
> Or is there a different way? In the spyglass selection box I cannot choose them, only the main map.
>
> Cheers,
> Wolfgang
>
>
> ----- Original Message -----
> From: "Marta Martinez"<mm...@cn...> <mailto:mm...@cn...>
> To: "Mailing list for Scipion users"<sci...@li...> <mailto:sci...@li...>
> Sent: Tuesday, 14 September, 2021 19:23:31
> Subject: Re: [scipion-users] import volumes with half maps question
>
> Hi Wolfgang,
>
> I've tested the import volumes protocol and I've had no problems with
> SCIPION v3.0.9-Eugenius.
>
> I think that you can solve your problem filling in the "Files
> directory" with the path of the main map
> (/Runs/000500_ProtRelionRefine3D/extra/relion_class001.mrc) and then
> the "Path half map1" and "Path half map2" with the respective paths
> (/Runs/000500_ProtRelionRefine3D/extra/relion_half1_class001_unfil.mrc
> and
> /Runs/000500_ProtRelionRefine3D/extra/relion_half2_class001_unfil.mrc). I've
> tested this example and it works. ("Pattern" box is empty).
>
> However, the two half maps that you can import this way are not
> SCIPION objects, just the main map. The half maps are attributes of
> the main map and then they will not be recognized as maps by other
> protocols. So, if you want to use any of those half maps as input for
> a job in SCIPION I recommend you to import each one independently in
> an individual import volumes protocol writing its respective whole
> path in the box "Files directory". Sorry for the inconvenience.
>
> With best wishes: MARTA
>
>
> Quoting "Lugmayr, Wolfgang"<w.l...@uk...> <mailto:w.l...@uk...>:
>
> Hi,
>
> I wanted to import 2 half-maps with the import volumes job.
>
> I selected the 2 maps with full path in the file browser and no
> files directory or pattern:
> When I press execute it says:
> - The path and pattern can not be both empty!!!
>
> When I set also the files directory - error:
> - Folders can not be selected.
> /home/lugmayr/foldername/
>
> When I set a file pattern + a files directory - error:
> - You can not use the options 'Pattern' and 'Set half maps' simultaneously
>
> Do I miss something here?
>
> How do I select a half map from a relion refinement job as input for a job?
>
> Cheers,
> Wolfgang
>
>
> --
> Universitätsklinikum Hamburg-Eppendorf (UKE)
> @ Centre for Structral Systems Biology (CSSB)
> @ Deutsches Elektronen-Synchrotron (DESY)
> Notkestrasse 85 Gebäude 15
> 22607 Hamburg, Germany
> Tel.: +49 40 8998-87652
> Email:wol...@cs... <mailto:wol...@cs...>
> http://www.cssb-hamburg.de/ <http://www.cssb-hamburg.de/>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li... <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li... <mailto:sci...@li...>
> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users>
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
|
|
From: Lugmayr, W. <w.l...@uk...> - 2021-09-15 12:16:22
|
Hi Pablo,
thank you and no worries, I prefer the solution part of your answers ;-)
I just wanted for curiosity compare the results of fsc3d, bsoft blocres and resmap.
the later two accept only real half-maps in their form.
I will try.
Cheers,
Wolfgang
From: "Pablo Conesa" <pc...@cn...>
To: "Mailing list for Scipion users" <sci...@li...>
Sent: Wednesday, 15 September, 2021 11:12:11
Subject: Re: [scipion-users] import volumes with half maps question
Forgot a "Hi Wolfgang!" or something similar. Now reading it looks rude. Extremely far from my intention and mood ;-) . Happy em processing!
On 15/9/21 10:53, Pablo Conesa wrote:
Halves imported as halves will never be seen by the spyglass. The "main" volume will have the two halves associated "internally" and protocols in need of the halves will seek for this internal structure. Therefore providing the "main" volume will provide, at the same time the internal halves associated.
Now, if you want to treat any half as a volume to be chosen from any spyglass button, then you need to import it as a "main" map.
There might be a case where a protocol does not "expect" halves to be associated to a volume. Only in this case you'll need to import halves as main volumes. But we try to prevent this to reduce number of clicks and improve clarity as usability.
Cheers!
On 15/9/21 9:31, Lugmayr, Wolfgang wrote:
BQ_BEGIN
Hi Marta,
yes it worked, I did not expect to enter a file when the UI says "Files directory".
Instead I tried to enter the file somehow in the "Pattern" input field.
Maybe the help hints can be extended?
Do I understand your description about half-maps attributes correctly?
When I need to select 2 half-maps for e.g. ResMap FSC, I have to import them from the Relion job as single imports?
Or is there a different way? In the spyglass selection box I cannot choose them, only the main map.
Cheers,
Wolfgang
----- Original Message -----
From: "Marta Martinez" [ mailto:mm...@cn... | <mm...@cn...> ] To: "Mailing list for Scipion users" [ mailto:sci...@li... | <sci...@li...> ] Sent: Tuesday, 14 September, 2021 19:23:31
Subject: Re: [scipion-users] import volumes with half maps question
Hi Wolfgang,
I've tested the import volumes protocol and I've had no problems with
SCIPION v3.0.9-Eugenius.
I think that you can solve your problem filling in the "Files
directory" with the path of the main map
(/Runs/000500_ProtRelionRefine3D/extra/relion_class001.mrc) and then
the "Path half map1" and "Path half map2" with the respective paths
(/Runs/000500_ProtRelionRefine3D/extra/relion_half1_class001_unfil.mrc
and
/Runs/000500_ProtRelionRefine3D/extra/relion_half2_class001_unfil.mrc). I've
tested this example and it works. ("Pattern" box is empty).
However, the two half maps that you can import this way are not
SCIPION objects, just the main map. The half maps are attributes of
the main map and then they will not be recognized as maps by other
protocols. So, if you want to use any of those half maps as input for
a job in SCIPION I recommend you to import each one independently in
an individual import volumes protocol writing its respective whole
path in the box "Files directory". Sorry for the inconvenience.
With best wishes: MARTA
Quoting "Lugmayr, Wolfgang" [ mailto:w.l...@uk... | <w.l...@uk...> ] :
BQ_BEGIN
Hi,
I wanted to import 2 half-maps with the import volumes job.
I selected the 2 maps with full path in the file browser and no
files directory or pattern:
When I press execute it says:
- The path and pattern can not be both empty!!!
When I set also the files directory - error:
- Folders can not be selected.
/home/lugmayr/foldername/
When I set a file pattern + a files directory - error:
- You can not use the options 'Pattern' and 'Set half maps' simultaneously
Do I miss something here?
How do I select a half map from a relion refinement job as input for a job?
Cheers,
Wolfgang
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Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
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