Hi,
I am trying to convert a star file (converted from cryosparc to relion using csparc2star.py from pyem) for re-extraction of recentered particles. relion_reconstruct has no problems with the file, but when I attempt to re-extract recentered particles, Relion complains that it is missing required parameters in the optics.star (but does not specify what these are). The conversion command I used was:
relion_convert_star --i P9_J215.star --o P9_J215_new.star --Cs 2.7 --Q0 0.1
I used the same command for both the micrograph and particle star files, and I’ve attached the beginning of both files for debugging.
I notice that relion_convert_star does not create an optics group column in the data_particles table of the star file. Should it do so?
Cheers
Oli
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# version 30001
data_optics
loop_
_rlnOpticsGroup #1
_rlnOpticsGroupName #2
_rlnAmplitudeContrast #3
_rlnSphericalAberration #4
_rlnVoltage #5
_rlnImagePixelSize #6
_rlnMicrographOriginalPixelSize #7
_rlnImageSize #8
_rlnImageDimensionality #9
1 opticsGroup0 0.100000 2.700000 300.000000 0.827500 0.827500 600 2
# version 30001
data_particles
loop_
_rlnImageName #1
_rlnMicrographName #2
_rlnCoordinateX #3
_rlnCoordinateY #4
_rlnAngleRot #5
_rlnAngleTilt #6
_rlnAnglePsi #7
_rlnDefocusU #8
_rlnDefocusV #9
_rlnDefocusAngle #10
_rlnPhaseShift #11
_rlnClassNumber #12
_rlnRandomSubset #13
_rlnOpticsGroup #14
_rlnOriginXAngst #15
_rlnOriginYAngst #16
[log in to unmask] csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00002Hln_00002Enn.frames_patch_aligned_doseweighted.mrc 2493.000000 4530.000000 -59.43837 103.514633 -120.36121 2899.840332 2819.877930 -28.24879 0.000000 1 1 1 4.732266 -7.21477
[log in to unmask] csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00002Hln_00002Enn.frames_patch_aligned_doseweighted.mrc 3584.000000 765.000000 21.344009 83.019714 55.912521 3689.104980 3609.142578 -28.24879 0.000000 1 1 1 -6.43898 -8.14570
[log in to unmask] csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00002Hln_00002Enn.frames_patch_aligned_doseweighted.mrc 1561.000000 3255.000000 114.085648 99.632111 152.295746 2927.461426 2847.499023 -28.24879 0.000000 1 1 1 -3.02555 -10.00758
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# version 30001
data_optics
loop_
_rlnOpticsGroup #1
_rlnOpticsGroupName #2
1 opticsGroup0
# version 30001
data_micrographs
loop_
_rlnMicrographName #1
_rlnOpticsGroup #2
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00002Hln_00002Enn.frames_patch_aligned_doseweighted.mrc 1
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00002Enn.frames_patch_aligned_doseweighted.mrc 1
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00005Enn.frames_patch_aligned_doseweighted.mrc 1
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00006Enn.frames_patch_aligned_doseweighted.mrc 1
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00007Enn.frames_patch_aligned_doseweighted.mrc 1
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00008Enn.frames_patch_aligned_doseweighted.mrc 1
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00010Enn.frames_patch_aligned_doseweighted.mrc 1
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00011Enn.frames_patch_aligned_doseweighted.mrc 1
csparc_mics/19oct14b_test_00004Gr_00015Sq_v01_00003Hln_00012Enn.frames_patch_aligned_doseweighted.mrc 1
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