Hi,
I am working on subtomogram averaging using Relion 2.1. Now I have a star file which contains CTF, Eular angles and center information of subtomogram 3D particles. I am trying to generate a map directly from this star file without any further refinement, just like relion_reconstruct on 2D particlres.
I read some previous messages in ccpem and know this can be done by using relion_refine without any re-alignments. So I tried to add --skip_align to the relion_refine command, but the result does not look right. Can anyone provide some details or exact command line about how to do it?
This is the command I tried:
relion_refine --i Refine3D/job752/run_data.star --o Refine3D/job752/test/run2 --ref reference.mrc --dont_combine_weights_via_disc --pool 3 --ctf --ctf_corrected_ref --iter 0 --tau2_fudge 4 --particle_diameter 350 --K 1 --flatten_solvent --zero_mask --strict_highres_exp 10 --sym C1 --norm --scale --j 8 --angpix 4.34 --skip_align
This is the information of the star file.
data_
loop_
_rlnMicrographName #1
_rlnCoordinateX #2
_rlnCoordinateY #3
_rlnCoordinateZ #4
_rlnImageName #5
_rlnCtfImage #6
_rlnGroupNumber #7
_rlnAngleRot #8
_rlnAngleTilt #9
_rlnAnglePsi #10
_rlnOriginX #11
_rlnOriginY #12
_rlnOriginZ #13
_rlnClassNumber #14
_rlnNormCorrection #15
_rlnLogLikeliContribution #16
_rlnMaxValueProbDistribution #17
_rlnNrOfSignificantSamples #18
_rlnRandomSubset #19
Tomograms/05_bin2_bp/IS002_291013_005.mrc 180.000000 1436.000000 52.000000 Extract/job339/Tomograms/05_bin2_bp/IS002_291013_005000001.mrc Particles/Tomograms/05/IS002_291013_005_ctf000001.mrc 1 -64.699252 27.240735 62.746452 -3.838082 -0.838082 -13.205582 1 1.000000 3.371628e+06 0.102490 16 1
Tomograms/05_bin2_bp/IS002_291013_005.mrc 216.000000 1348.000000 52.000000 Extract/job339/Tomograms/05_bin2_bp/IS002_291013_005000002.mrc Particles/Tomograms/05/IS002_291013_005_ctf000002.mrc 1 -66.147951 23.310485 -150.017528 -1.389332 -2.573082 -14.205582 1 1.000000 3.372551e+06 0.127196 7 2
Tomograms/05_bin2_bp/IS002_291013_005.mrc 320.000000 1252.000000 64.000000 Extract/job339/Tomograms/05_bin2_bp/IS002_291013_005000003.mrc Particles/Tomograms/05/IS002_291013_005_ctf000003.mrc 1 -65.990381 30.830989 -116.578173 0.161918 0.794418 -9.838082 1 1.000000 3.365377e+06 0.202417 9 1
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