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Hi Takanori, Thanks for the reply. I'm also interested in this process, although not going to a newer version of relion. In my case, my old project started from pre-Motioncorred (and bin4) micrographs, and now I would like to start a new project from raw data. I already imported and Motioncorred the raw images and would like to re-extract using the run_data.star file from my old project folder. I do understand that I need to modify the coordinates at the first two columns, as well as _rlnMicrographName #9. I'm just curious if parameters like HelicalTubeID, ImageName or anything else also need to be adjusted (yes, this is helical processing work)? I'm also curious about what info was read in this re-extraction job and whether the sampling/tilt are retained after re-extracting. Also, I assume the coordinates in the data.star are for particles, right? Should I just ignore the Helix tab when extracting? Best, Qiuye On Mon, Oct 21, 2019 at 11:56 PM Takanori Nakane <[log in to unmask]> wrote: > Hi, > > Please look at this: > https://github.com/3dem/relion/issues/524 > > Best regards, > > Takanori Nakane > > On 2019/10/22 2:36, Alpay Burak Seven wrote: > > Hi > > > > I imported run_it0025_data.star file from a Class3D job from Relion3.0.7 > > to Relion3.1. > > Then I am trying to extract from the particles in a new relion project > > folder from micrographs for which motioncor and ctffind is done with the > > relion3.1 in this new project folder. > > > > I am getting box sizes not available error. > > > > Is anyone aware of this error? > > > > What is the easiest way to get the particle coordinates from an old > > relion project folder to a new relion3.1 project folder? > > > > Thank you > > > > Alpay > > > > Here is the entire error message > > RELION version: 3.1-beta-commit-a6aaa5 > > > > Error: > > in: > > > /share/PI/yiorgo/alpay/sourcecode/Relion/3.191015/relion/src/jaz/obs_model.cpp, > > > line 650 > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > === Backtrace === > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x66) > > > [0x42f356] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZNK16ObservationModel10getBoxSizeEi+0x5b) > > > [0x46e45b] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0x3ae1) > > > [0x456ae1] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x7e1) > > > [0x457b11] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x370) > > > [0x467cc0] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12) > > > [0x468142] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(main+0x3b) > > > [0x42442b] > > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fb94b50c495] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi() > > > [0x424d7f] > > ================== > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > in: > > > /share/PI/yiorgo/alpay/sourcecode/Relion/3.191015/relion/src/jaz/obs_model.cpp, > > > line 650 > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > === Backtrace === > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x66) > > > [0x42f356] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZNK16ObservationModel10getBoxSizeEi+0x5b) > > > [0x46e45b] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0x3ae1) > > > [0x456ae1] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x7e1) > > > [0x457b11] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x370) > > > [0x467cc0] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12) > > > [0x468142] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(main+0x3b) > > > [0x42442b] > > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fd9e468f495] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi() > > > [0x424d7f] > > ================== > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > in: > > > /share/PI/yiorgo/alpay/sourcecode/Relion/3.191015/relion/src/jaz/obs_model.cpp, > > > line 650 > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > in: > > > /share/PI/yiorgo/alpay/sourcecode/Relion/3.191015/relion/src/jaz/obs_model.cpp, > > > line 650 > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > === Backtrace === > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x66) > > > [0x42f356] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZNK16ObservationModel10getBoxSizeEi+0x5b) > > > [0x46e45b] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0x3ae1) > > > [0x456ae1] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x7e1) > > > [0x457b11] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x370) > > > [0x467cc0] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12) > > > [0x468142] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(main+0x3b) > > > [0x42442b] > > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f67ac8e0495] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi() > > > [0x424d7f] > > ================== > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > === Backtrace === > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x66) > > > [0x42f356] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZNK16ObservationModel10getBoxSizeEi+0x5b) > > > [0x46e45b] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0x3ae1) > > > [0x456ae1] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x7e1) > > > [0x457b11] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x370) > > > [0x467cc0] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12) > > > [0x468142] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(main+0x3b) > > > [0x42442b] > > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f2d2d4b9495] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi() > > > [0x424d7f] > > ================== > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > in: > > > /share/PI/yiorgo/alpay/sourcecode/Relion/3.191015/relion/src/jaz/obs_model.cpp, > > > line 650 > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > === Backtrace === > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x66) > > > [0x42f356] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZNK16ObservationModel10getBoxSizeEi+0x5b) > > > [0x46e45b] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0x3ae1) > > > [0x456ae1] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x7e1) > > > [0x457b11] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x370) > > > [0x467cc0] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12) > > > [0x468142] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(main+0x3b) > > > [0x42442b] > > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f479996f495] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi() > > > [0x424d7f] > > ================== > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > in: > > > /share/PI/yiorgo/alpay/sourcecode/Relion/3.191015/relion/src/jaz/obs_model.cpp, > > > line 650 > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > in: > > > /share/PI/yiorgo/alpay/sourcecode/Relion/3.191015/relion/src/jaz/obs_model.cpp, > > > line 650 > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > === Backtrace === > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x66) > > > [0x42f356] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZNK16ObservationModel10getBoxSizeEi+0x5b) > > > [0x46e45b] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0x3ae1) > > > [0x456ae1] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x7e1) > > > [0x457b11] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x370) > > > [0x467cc0] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12) > > > [0x468142] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(main+0x3b) > > > [0x42442b] > > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f4ab1620495] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi() > > > [0x424d7f] > > ================== > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > in: > > > /share/PI/yiorgo/alpay/sourcecode/Relion/3.191015/relion/src/jaz/obs_model.cpp, > > > line 650 > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > === Backtrace === > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x66) > > > [0x42f356] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZNK16ObservationModel10getBoxSizeEi+0x5b) > > > [0x46e45b] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0x3ae1) > > > [0x456ae1] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x7e1) > > > [0x457b11] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x370) > > > [0x467cc0] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12) > > > [0x468142] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(main+0x3b) > > > [0x42442b] > > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7faef186a495] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi() > > > [0x424d7f] > > ================== > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > === Backtrace === > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x66) > > > [0x42f356] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZNK16ObservationModel10getBoxSizeEi+0x5b) > > > [0x46e45b] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing33extractParticlesFromOneMicrographER13MetaDataTable8FileNameiS2_S2_RllRdS4_S4_S4_+0x3ae1) > > > [0x456ae1] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN13Preprocessing31extractParticlesFromFieldOfViewE8FileNamel+0x7e1) > > > [0x457b11] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x370) > > > [0x467cc0] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x12) > > > [0x468142] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi(main+0x3b) > > > [0x42442b] > > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7feba3826495] > > > /share/PI/yiorgo/alpay/modules/alpaysprograms/myRelion/3.191015/bin/relion_preprocess_mpi() > > > [0x424d7f] > > ================== > > ERROR: > > ObservationModel::getBoxSize: box sizes not available > > > > srun: Job step aborted: Waiting up to 32 seconds for job step to finish. > > slurmstepd: error: *** STEP 53051185.0 ON sh-106-57 CANCELLED AT > > 2019-10-21T18:04:32 *** > > srun: error: sh-106-57: tasks 0-7: Exited with exit code 1 > > srun: Terminating job step 53051185.0 > > srun: error: sh-106-57: tasks 8-23: Killed > > > > > > > > ------------------------------------------------------------------------ > > > > To unsubscribe from the CCPEM list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 > > > > ######################################################################## > > To unsubscribe from the CCPEM list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 > ######################################################################## To unsubscribe from the CCPEM list, click the following 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