I need help. Thanks in advance.
Hi Daniel:
My colleague Elmar has been using CryoSPRAC at OHSU and ran into an issue (using cs files in Relion after converting it to star). I could not resolve it myself. His notes on the issue:
I run CryoSPARC v2.15.0+200710.
I try to convert cs files to star files that I would be able to read, either with relion 3.1.0-commit-72f783 or relion 3.0.7
I generated star files in 3 ways:
-
executing an export job in cryosparc and then:
csparc2star.py P2_J12_particles_exported.cs P2_J12_particles_exported_relion31.star
csparc2star.py -r2 P2_J12_particles_exported.cs P2_J12_particles_exported_relion30.star -
csparc2star.py cryosparc_P2_J12_020_particles.cs P2_J12_passthrough_particles.cs cryosparc_P2_J12_020_particles_passthrough_relion31.star
csparc2star.py -r2 cryosparc_P2_J12_020_particles.cs P2_J12_passthrough_particles.cs cryosparc_P2_J12_020_particles_passthrough_relion30.star -
csparc2star.py cryosparc_P2_J12_020_particles.cs cryosparc_P2_J12_020_relion31.star
csparc2star.py -r2 cryosparc_P2_J12_020_particles.cs cryosparc_P2_J12_020_relion30.star
It does not matter, which of the 3 version I take.
If I try to load a relion 31 compatible star file into relion 31 I get the error:
=== Backtrace ===
/sw/relion/3.1/bin/relion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x529ce1]
/sw/relion/3.1/bin/relion_refine(_ZNK16ObservationModel10getBoxSizeEi+0x6b) [0x5769eb]
/sw/relion/3.1/bin/relion_refine(_ZN7MlModel20initialiseFromImagesE8FileNamebR10ExperimentRbS3_S3_dbbb+0x605) [0x50d115]
/sw/relion/3.1/bin/relion_refine(_ZN11MlOptimiser17initialiseGeneralEi+0x4f1) [0x47ca91]
/sw/relion/3.1/bin/relion_refine(_ZN11MlOptimiser10initialiseEv+0x484) [0x47f8c4]
/sw/relion/3.1/bin/relion_refine(main+0x33) [0x430f83]
/lib64/libc.so.6(__libc_start_main+0xf3) [0x7fd4360421a3]
/sw/relion/3.1/bin/relion_refine() [0x4343ff]
ERROR:
ObservationModel::getBoxSize: box sizes not available. Make sure particle images are available before converting/importing STAR files from earlier versions of RELION.
If I try ti load a relion 30 compatible star file into relion 30 I get the error:
in: /sw/relion/relion-3.0-src/src/image.h, line 175
=== Backtrace ===
/sw/relion/3.0/bin/relion_refine(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x438941]
/sw/relion/3.0/bin/relion_refine() [0x43a3a6]
/sw/relion/3.0/bin/relion_refine(_ZN5ImageIdE4readERK8FileNameblbb+0xce) [0x498ace]
/sw/relion/3.0/bin/relion_refine(_ZN10Experiment4readE8FileNamebbbb+0x8f5) [0x4e6ae5]
/sw/relion/3.0/bin/relion_refine(_ZN11MlOptimiser17initialiseGeneralEi+0x43a) [0x4632fa]
/sw/relion/3.0/bin/relion_refine(_ZN11MlOptimiser10initialiseEv+0x484) [0x46f4a4]
/sw/relion/3.0/bin/relion_refine(main+0xb03) [0x42b083]
/lib64/libc.so.6(__libc_start_main+0xf3) [0x7f3b8df071a3]
/sw/relion/3.0/bin/relion_refine() [0x42e3cf]
ERROR:
Cannot read file J10/extract/1782638280813807455_14sep05c_00024sq_00003hl_00005es.frames_patch_aligned_doseweighted_particles.mrc It does not exist
Is there any obvious thing I do wrong?
How could I get this running?
Any help is appreciated.
Thanks
āKumar, Ryan, Elmar
kumar@healthtechnologyinnovations,.com
ryan@healthtechnologyinnovations.com
buchere@ohsu.edu