Hey Everyone,
We have been having problems using multiple MPI proc on Relion 1.3 during 2D classification, 3D classification, and 3D autorefine. The program will allow us to use multiple threads, but we cannot increase the MPI proc above 1. We installed openMPI and relion according to the websites' directions. We have even tested our openMPI using a simple test script showing that it works properly. The error occurs after the first iteration. If we lower the MPI to 1, then an error won't occur after the first iteration, and the calculation will finish properly.
Does anyone have suggestions? We have been stumped on this for a few weeks now.
Best Wishes,
Ali Khan
P.S. Here is the output when the error occurs:
Executing: mpirun -n 30 `which relion_refine_mpi` --o Class3D/run1 --i particles_autopick_sort4_class2d.star --particle_diameter 200 --angpix 1.482 --ref Cx26-channel_60A.mrc --firstiter_cc --ini_high 50 --ctf --ctf_corrected_ref --iter 25 --tau2_fudge 2 --K 4 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale --j 1 --memory_per_thread 2 &
=== RELION MPI setup ===
+ Number of MPI processes = 30
+ Master (0) runs on host = knoll
+ Slave 1 runs on host = knoll
+ Slave 2 runs on host = knoll
+ Slave 3 runs on host = knoll
+ Slave 4 runs on host = knoll
+ Slave 5 runs on host = knoll
+ Slave 6 runs on host = knoll
+ Slave 7 runs on host = knoll
+ Slave 8 runs on host = knoll
+ Slave 9 runs on host = knoll
+ Slave 10 runs on host = knoll
+ Slave 11 runs on host = knoll
+ Slave 12 runs on host = knoll
+ Slave 13 runs on host = knoll
+ Slave 14 runs on host = knoll
+ Slave 15 runs on host = knoll
+ Slave 16 runs on host = knoll
+ Slave 17 runs on host = knoll
+ Slave 18 runs on host = knoll
+ Slave 19 runs on host = knoll
+ Slave 20 runs on host = knoll
+ Slave 21 runs on host = knoll
+ Slave 22 runs on host = knoll
+ Slave 23 runs on host = knoll
+ Slave 24 runs on host = knoll
+ Slave 25 runs on host = knoll
+ Slave 26 runs on host = knoll
+ Slave 27 runs on host = knoll
+ Slave 28 runs on host = knoll
+ Slave 29 runs on host = knoll
=================
Estimating initial noise spectra
000/??? sec ~~(,_,"> [o1.33/1.33 min ...........................................................~~(,_,"1.33/1.33 min ............................................................~~(,_,">
WARNING: There are only 4 particles in group 32
WARNING: There are only 2 particles in group 123
WARNING: There are only 4 particles in group 128
WARNING: There are only 4 particles in group 244
WARNING: There are only 3 particles in group 267
WARNING: There are only 4 particles in group 303
WARNING: There are only 4 particles in group 344
WARNING: There are only 4 particles in group 383
WARNING: There are only 4 particles in group 458
WARNING: There are only 4 particles in group 479
WARNING: There are only 3 particles in group 493
WARNING: There are only 1 particles in group 532
WARNING: There are only 4 particles in group 537
WARNING: There are only 4 particles in group 538
WARNING: There are only 4 particles in group 544
WARNING: There are only 3 particles in group 551
WARNING: There are only 4 particles in group 566
WARNING: There are only 4 particles in group 601
WARNING: There are only 3 particles in group 613
WARNING: There are only 1 particles in group 617
WARNING: There are only 4 particles in group 629
WARNING: There are only 4 particles in group 643
WARNING: There are only 1 particles in group 655
WARNING: There are only 4 particles in group 690
WARNING: There are only 4 particles in group 710
WARNING: There are only 4 particles in group 796
WARNING: There are only 3 particles in group 840
WARNING: There are only 3 particles in group 876
WARNING: There are only 4 particles in group 882
WARNING: There are only 3 particles in group 914
WARNING: There are only 3 particles in group 927
WARNING: There are only 4 particles in group 935
WARNING: There are only 4 particles in group 988
WARNING: There are only 3 particles in group 1009
WARNING: There are only 4 particles in group 1026
WARNING: There are only 4 particles in group 1045
WARNING: There are only 2 particles in group 1046
WARNING: There are only 1 particles in group 1048
WARNING: There are only 4 particles in group 1062
WARNING: There are only 2 particles in group 1064
WARNING: There are only 2 particles in group 1065
WARNING: There are only 4 particles in group 1068
WARNING: There are only 4 particles in group 1069
WARNING: There are only 3 particles in group 1070
WARNING: There are only 3 particles in group 1078
WARNING: There are only 4 particles in group 1082
WARNING: There are only 3 particles in group 1083
WARNING: There are only 3 particles in group 1089
WARNING: There are only 4 particles in group 1092
WARNING: There are only 4 particles in group 1093
WARNING: There are only 1 particles in group 1094
WARNING: There are only 2 particles in group 1095
WARNING: There are only 3 particles in group 1097
WARNING: There are only 1 particles in group 1098
WARNING: There are only 1 particles in group 1099
WARNING: You may want to consider joining some micrographs into larger groups to obtain more robust noise estimates.
You can do so by using the same rlnMicrographName for particles from multiple different micrographs in the input STAR file.
It is then best to join micrographs with similar defocus values and similar apparent signal-to-noise ratios.
CurrentResolution= 49.7952 Angstroms, which requires orientationSampling of at least 27.6923 degrees for a particle of diameter 200 Angstroms
Oversampling= 0 NrHiddenVariableSamplingPoints= 387072
OrientationalSampling= 15 NrOrientations= 4608
TranslationalSampling= 2 NrTranslations= 21
=============================
Oversampling= 1 NrHiddenVariableSamplingPoints= 12386304
OrientationalSampling= 7.5 NrOrientations= 36864
TranslationalSampling= 1 NrTranslations= 84
=============================
Estimated memory for expectation step > 0.857207 Gb, available memory = 2 Gb.
Estimated memory for maximization step > 0.00851655 Gb, available memory = 2 Gb.
Expectation iteration 1 of 25
000/??? sec ~~(,_,"> [o8.67/8.80 min ...........................................................~~(,_,"8.78/8.80 min ...........................................................~~(,_,"8.93/8.93 min ............................................................~~(,_,">
Maximization ...
000/??? sec ~~(,_,"> [o 6/ 6 sec ............................................................~~(,_,">
Estimating accuracies in the orientational assignment ...
000/??? sec ~~(,_,"> [o 31/ 31 sec ...........................................................~~(,_," 31/ 31 sec ...........................................................~~(,_," 31/ 31 sec ...........................................................~~(,_," 31/ 31 sec ...........................................................~~(,_," 31/ 31 sec ...........................................................~~(,_," 31/ 31 sec ...........................................................~~(,_," 31/ 31 sec ............................................................~~(,_,">
Auto-refine: Estimated accuracy angles= 19.8 degrees; offsets= 6.09 pixels
Auto-refine: WARNING: The angular accuracy is worse than 10 degrees, so basically you cannot align your particles (yet)!
Auto-refine: WARNING: You probably need not worry if the accuracy improves during the next few iterations.
Auto-refine: WARNING: However, if the problem persists it may lead to spurious FSC curves, so be wary of inflated resolution estimates...
Auto-refine: WARNING: Sometimes it is better to tune resolution yourself by adjusting T in a 3D-classification with a single class.
CurrentResolution= 49.7952 Angstroms, which requires orientationSampling of at least 27.6923 degrees for a particle of diameter 200 Angstroms
Oversampling= 0 NrHiddenVariableSamplingPoints= 387072
OrientationalSampling= 15 NrOrientations= 4608
TranslationalSampling= 2 NrTranslations= 21
=============================
Oversampling= 1 NrHiddenVariableSamplingPoints= 12386304
OrientationalSampling= 7.5 NrOrientations= 36864
TranslationalSampling= 1 NrTranslations= 84
=============================
Estimated memory for expectation step > 0.857207 Gb, available memory = 2 Gb.
Estimated memory for maximization step > 0.00851655 Gb, available memory = 2 Gb.
Expectation iteration 2 of 25
000/??? sec ~~(,_,"> [oo] exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_part_id= 4191exp_iimage=1
group_id= 1020 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 15.2914
exp_part_id= 3811exp_iimage=1
group_id= 974 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
0
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wsum_model.pdf_direction[exp_ipart]=
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mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 17.8113
exp_thisparticle_sumweight= 0
exp_part_id= 9486exp_iimage=1
group_id= 359 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 17.4846
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_part_id= 9945exp_iimage=1
group_id= 147 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
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0
0
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0
0
0
0
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0
0
0
0
0
0
0
wsum_model.pdf_direction[exp_ipart]=
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
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0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 14.9149
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
exp_thisparticle_sumweight= 0
slave 2 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
slave 6 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
slave 16 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
slave 5 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : --iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--pool (8) : Number of images to be processed together
--dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step
--dont_check_norm (false) : Skip the check whether the images are normalised correctly
--sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models?
--temp_ini (1000) : Initial temperature (K) for simulated --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--pool (8) : Number of images to be processed together
--dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step
--dont_check_norm (false) : Skip the check whether the images are normalised correctly
--sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models?
--temp_ini (1000) : Initial temperature (K) for simulated annealing
--temp_fin (1) : Initial temperature (K) for simulated annealing
--always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?)
--scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files
annealing
--temp_fin (1) : Initial temperature (K) for simulated annealing
--always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?)
--scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--pool (8) : Number of images to be processed together
--dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step
--dont_check_norm (false) : Skip the check whether the images are normalised correctly
--sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models?
--temp_ini (1000) : Initial temperature (K) for simulated annealing
--temp_fin (1) : Initial temperature (K) for simulated annealing
--always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?)
--scratchdir () : Directory --offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--pool (8) : Number of images to be processed together
--dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step
--dont_check_norm (false) : Skip the check whether the images are normalised correctly
--sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models?
--temp_ini (1000) : Initial temperature (K) for simulated annealing
--temp_fin (1) : Initial temperature (K) for simulated annealing
--always_cc (false) : Perform CC-calculation in all iterations ( (with absolute path, and visible to all nodes) for temporary files
useful for faster denovo model generation?)
--scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files
exp_part_id= 2344exp_iimage=1
group_id= 653 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
0
0
0
0
0
0
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wsum_model.pdf_direction[exp_ipart]=
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mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 17.4735
slave 8 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--pool (8) : Number of images to be processed together
--dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step
--dont_check_norm (false) : Skip the check whether the images are normalised correctly
--sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models?
--temp_ini (1000) : Initial temperature (K) for simulated annealing
--temp_fin (1) : Initial temperature (K) for simulated annealing
--always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?)
--scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 5 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
exp_part_id= 7762exp_iimage=1
group_id= 1050 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 9151exp_iimage=1
group_id= 501 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 5367exp_iimage=1
group_id= 790 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 10181exp_iimage=1
group_id= 571 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 9552exp_iimage=1
group_id= 631 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
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4.5e-06
4.3e-06
4e-06
3.8e-06
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3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 10584exp_iimage=1
group_id= 1039 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
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0.00034
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0.00018
0.00012
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8.3e-05
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7e-05
6.4e-05
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4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
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4.5e-06
4.3e-06
4e-06
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3e-06
2.9e-06
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2.1e-06
2e-06
2e-06
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1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 10236exp_iimage=1
group_id= 57 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
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7e-05
6.4e-05
5.8e-05
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4.9e-05
4.6e-05
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3.5e-05
3.3e-05
3e-05
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2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
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4.5e-06
4.3e-06
4e-06
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3e-06
2.9e-06
2.7e-06
2.6e-06
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2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 6910exp_iimage=1
group_id= 404 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
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7e-05
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5.8e-05
5.4e-05
4.9e-05
4.6e-05
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3.8e-05
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3.3e-05
3e-05
2.7e-05
2.5e-05
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2e-05
1.8e-05
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1.4e-05
1.3e-05
1.2e-05
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1.1e-05
9.9e-06
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8.6e-06
8e-06
7.5e-06
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3e-06
2.9e-06
2.7e-06
2.6e-06
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2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 7586exp_iimage=1
group_id= 378 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
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1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
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4e-06
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3.3e-06
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3e-06
2.9e-06
2.7e-06
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2.5e-06
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2e-06
2e-06
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1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 1311exp_iimage=1
group_id= 699 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 11170exp_iimage=1
group_id= 422 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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exp_part_id= 4689exp_iimage=1
group_id= 883 mymodel.scale_correction[group_id]= 1
exp_ipass= 0
sampling.NrDirections(0, true)= 192 sampling.NrDirections(0, false)= 192
sampling.NrPsiSamplings(0, true)= 24 sampling.NrPsiSamplings(0, false)= 24
mymodel.sigma2_noise[exp_ipart]=
0.00029
0.00047
0.00055
0.00034
0.00045
0.00038
0.00034
0.00026
0.00018
0.00012
0.0001
0.0001
9.4e-05
8.3e-05
7.5e-05
7e-05
6.4e-05
5.8e-05
5.4e-05
4.9e-05
4.6e-05
4.2e-05
3.8e-05
3.5e-05
3.3e-05
3e-05
2.7e-05
2.5e-05
2.3e-05
2.2e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.1e-05
1.1e-05
9.9e-06
9.2e-06
8.6e-06
8e-06
7.5e-06
7e-06
6.6e-06
6.1e-06
5.8e-06
5.4e-06
5.1e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.6e-06
3.5e-06
3.3e-06
3.1e-06
3e-06
2.9e-06
2.7e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
2e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.6e-06
1.6e-06
1.6e-06
1.5e-06
1.5e-06
1.5e-06
1.4e-06
1.4e-06
1.4e-06
1.4e-06
wsum_model.sigma2_noise[exp_ipart]=
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wsum_model.pdf_direction[exp_ipart]=
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mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 17.3356
slave 27 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 17.0046
slave 15 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for loca 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 20.6211
slave 25 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 18.2858
slave 24 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 17.3002
slave 17 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for loc 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 15.1631
slave 12 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local--------------------------------------------------------------------------
mpirun has exited due to process rank 6 with PID 10918 on
node knoll exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[knoll:10910] 16 more processes have sent help message help-mpi-api.txt / mpi-abort
[knoll:10910] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 14.1625
slave 23 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for loca 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 17.548
slave 13 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 17.0534
slave 28 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 18.9231
slave 9 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 16.2506
slave 29 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
mymodel.avg_norm_correction= 4265.73
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= 0
exp_min_diff2[exp_ipart]= 14.803
slave 19 encountered error: ERROR!!! zero sum of weights....
File: src/ml_optimiser.cpp line: 3982
+++ RELION: command line arguments (with defaults for optional ones between parantheses) +++
====== General options =====
--i : Input images (in a star-file or a stack)
--o : Output rootname
--angpix : Pixel size (in Angstroms)
--iter (50) : Maximum number of iterations to perform
--tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data)
--K (1) : Number of references to be refined
--particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms)
--zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise)
--flatten_solvent (false) : Perform masking on the references as well?
--solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter)
--solvent_mask2 (None) : User-provided secondary mask (with its own average density)
--tau (None) : STAR file with input tau2-spectrum (to be kept constant)
--split_random_halves (false) : Refine two random halves of the data completely separately
--low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations
====== Initialisation =====
--ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!)
--offset (3) : Initial estimated stddev for the origin offsets
--firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale)
--ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration
====== Orientations =====
--oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc)
--healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc
--psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D)
--limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views
--sym (c1) : Symmetry group
--offset_range (6) : Search range for origin offsets (in pixels)
--offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels)
--perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb)
--auto_refine (false) : Perform 3D auto-refine procedure?
--auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches
--sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev)
--sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev)
--sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev)
--sigma_psi (-1) : Stddev on the in-plane angle for local al angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--pool (8) : Number of images to be processed together
--dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step
--dont_check_norm (false) : Skip the check whether the images are normalised correctly
--sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models?
--temp_ini (1000) : Initial temperature (K) for simulated annealing
--temp_fin (1) : Initial temperature (K) for simulated annealing
--always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?)
--scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files
angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--pool (8) : Number of images to be processed together
--dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step
--dont_check_norm (false) : Skip the check whether the images are normalised correctly
--sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models?
--temp_ini (1000) : Initial temperature (K) for simulated annealing
--temp_fin (1) : Initial temperature (K) for simulated annealing
--always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?)
--scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files
angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--pool (8) : Number of images to be processed together
--dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step
--dont_check_norm (false) : Skip the check whether the images are normalised correctly
--sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models?
--temp_ini (1000) : Initial temperature (K) for simulated annealing
--temp_fin (1) : Initial temperature (K) for simulated annealing
--always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?)
--scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files
l angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--pool (8) : Number of images to be processed together
--dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step
--dont_check_norm (false) : Skip the check whether the images are normalised correctly
--sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models?
--temp_ini (1000) : Initial temperature (K) for simulated annealing
--temp_fin (1) : Initial temperature (K) for simulated annealing
--always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?)
--scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files
angular searches (of +/- 3 stddev)
--skip_align (false) : Skip orientational assignment (only classify)?
--skip_rotate (false) : Skip rotational assignment (only translate and classify)?
====== Corrections =====
--ctf (false) : Perform CTF correction?
--ctf_intact_first_peak (false) : Ignore CTFs until their first peak?
--ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected?
--ctf_phase_flipped (false) : Have the data been CTF phase-flipped?
--only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction)
--norm (false) : Perform normalisation-error correction?
--scale (false) : Perform intensity-scale corrections on image groups?
====== Computation =====
--j (1) : Number of threads to run in parallel (only useful on multi-core machines)
--memory_per_thread (2) : Available RAM (in Gb) for each thread
--pool (8) : Number of images to be processed together
--dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc
====== Expert options =====
--pad (2) : Oversampling factor for the Fourier transforms of the references
--NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation?
--r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation
--verb (1) : Verbosity (1=normal, 0=silent)
--random_seed (-1) : Number for the random seed generator
--coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach
--adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling
--maskedge (5) : Width of the soft edge of the spherical mask (in pixels)
--fix_sigma_noise (false) : Fix the experimental noise spectra?
--fix_sigma_offset (false) : Fix the stddev in the origin offsets?
--incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement
--print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit
--print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit
--strict_highres_exp (-1) : Resolution limit (in Angstrom) to restrict probability calculations in the expectation step
--dont_check_norm (false) : Skip the check whether the images are normalised correctly
--sim_anneal (false) : Perform simulated-annealing to improve overall convergence of random starting models?
--temp_ini (1000) : Initial temperature (K) for simulated annealing
--temp_fin (1) : Initial temperature (K) for simulated annealing
--always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?)
--scratchdir () : Directory (with absolute path, and visible to all nodes) for temporary files
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