Hi,
I am new relion user. I have been having trouble with the 2D classification. I can perform the first iteration, but the program will crash at the start of the 2nd iteration. I have tried using smaller data sets of particles, running to generate larger and smaller amount of classes, changing the regularisation parameters, and playing with various MPI:thread combinations, but I still get the same error. Here is the output from the job:
ali@knoll:~/Jobs/Relion/20141009_Cx26onholes_krios$ Executing: mpirun -n 15 `which relion_refine_mpi` --o Class2D/autopick_sort2 --i particles_autopick_sort2.star --particle_diameter 200 --angpix 1.482 --ctf --iter 25 --tau2_fudge 2 --K 100 --flatten_solvent --zero_mask --oversampling 1 --psi_step 10 --offset_range 5 --offset_step 2 --norm --scale --j 2 --memory_per_thread 4 &
=== RELION MPI setup ===
+ Number of MPI processes = 15
+ Number of threads per MPI process = 2
+ Total number of threads therefore = 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
=================
Estimating initial noise spectra
3/ 3 sec ............................................................~~(,_,">
WARNING: There are only 4 particles in group 165
WARNING: There are only 3 particles in group 843
WARNING: There are only 4 particles in group 868
WARNING: There are only 4 particles in group 869
WARNING: There are only 1 particles in group 1030
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.
Estimating accuracies in the orientational assignment ...
43/ 43 sec ............................................................~~(,_,">
Auto-refine: Estimated accuracy angles= 30.1 degrees; offsets= 10.1 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= 20.748 Angstroms, which requires orientationSampling of at least 11.6129 degrees for a particle of diameter 200 Angstroms
Oversampling= 0 NrHiddenVariableSamplingPoints= 75600
OrientationalSampling= 10 NrOrientations= 36
TranslationalSampling= 2 NrTranslations= 21
=============================
Oversampling= 1 NrHiddenVariableSamplingPoints= 2419200
OrientationalSampling= 5 NrOrientations= 288
TranslationalSampling= 1 NrTranslations= 84
=============================
Estimated memory for expectation step > 0.25979 Gb, available memory = 8 Gb.
Estimated memory for maximization step > 0.000280693 Gb, available memory = 8 Gb.
Expectation iteration 1 of 25
10.40/10.40 min ............................................................~~(,_,">
Maximization ...
0/ 0 sec ............................................................~~(,_,">
Estimating accuracies in the orientational assignment ...
25/ 25 sec ............................................................~~(,_,">
Auto-refine: Estimated accuracy angles= 30.1 degrees; offsets= 10.1 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= 75600
OrientationalSampling= 10 NrOrientations= 36
TranslationalSampling= 2 NrTranslations= 21
=============================
Oversampling= 1 NrHiddenVariableSamplingPoints= 2419200
OrientationalSampling= 5 NrOrientations= 288
TranslationalSampling= 1 NrTranslations= 84
=============================
Estimated memory for expectation step > 0.251706 Gb, available memory = 8 Gb.
Estimated memory for maximization step > 0.000135183 Gb, available memory = 8 Gb.
Expectation iteration 2 of 25
000/??? sec ~~(,_,"> [oo] exp_thisparticle_sumweight= -nan
exp_thisparticle_sumweight= -nan
exp_thisparticle_sumweight= -nan
exp_part_id= 480exp_iimage=1
group_id= 15 mymodel.scale_correction[group_id]= 0.950691
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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
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wsum_model.pdf_direction[exp_ipart]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 5.45461
slave 7 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 7 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= 7099exp_iimage=1
group_id= 231 mymodel.scale_correction[group_id]= 0.876464
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 4.10698
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)
--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
exp_part_id= 6002exp_iimage=1
group_id= 200 mymodel.scale_correction[group_id]= 0.980965
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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
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0
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0
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wsum_model.pdf_direction[exp_ipart]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 6.22402
slave 1 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
exp_thisparticle_sumweight= -nan
exp_part_id= 1328exp_iimage=1
group_id= 42 mymodel.scale_correction[group_id]= 0.944879
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
wsum_model.pdf_direction[exp_ipart]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 6.28488
slave 3 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
====== Initiali exp_thisparticle_sumweight= -nan
exp_part_id= 28074exp_iimage=1
group_id= 937 mymodel.scale_correction[group_id]= 1.08193
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
wsum_model.pdf_direction[exp_ipart]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 5.85256
slave 4 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
====== Initial exp_thisparticle_sumweight= -nan
exp_thisparticle_sumweight= -nan
exp_thisparticle_sumweight= -nan
exp_part_id= 18413exp_iimage=1
group_id= 598 mymodel.scale_correction[group_id]= 0.989704
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
wsum_model.pdf_direction[exp_ipart]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 5.4342
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
====== Initial exp_thisparticle_sumweight= -nan
exp_part_id= 5691exp_iimage=1
group_id= 189 mymodel.scale_correction[group_id]= 1.01945
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
wsum_model.pdf_direction[exp_ipart]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 6.40273
slave 10 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
====== Initial exp_thisparticle_sumweight= -nan
exp_part_id= 26950exp_iimage=1
group_id= 898 mymodel.scale_correction[group_id]= 1.01818
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
wsum_model.pdf_direction[exp_ipart]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 5.7247
slave 11 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
====== Initial exp_thisparticle_sumweight= -nan
exp_part_id= 12644exp_iimage=1
group_id= 395 mymodel.scale_correction[group_id]= 1.03731
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
wsum_model.pdf_direction[exp_ipart]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 5.86771
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
====== Initia exp_thisparticle_sumweight= -nan
exp_part_id= 13423exp_iimage=1
group_id= 425 mymodel.scale_correction[group_id]= 0.892488
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
wsum_model.pdf_direction[exp_ipart]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 4.40258
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
====== Initi exp_thisparticle_sumweight= -nan
exp_part_id= 26800exp_iimage=1
group_id= 892 mymodel.scale_correction[group_id]= 1.01436
exp_ipass= 0
sampling.NrDirections(0, true)= 1 sampling.NrDirections(0, false)= 1
sampling.NrPsiSamplings(0, true)= 36 sampling.NrPsiSamplings(0, false)= 36
mymodel.sigma2_noise[exp_ipart]=
0.00054
0.0005
0.00061
0.00038
0.00041
0.00037
0.00032
0.00025
0.0002
0.00014
9.7e-05
8.8e-05
8.7e-05
9.2e-05
7.7e-05
6.4e-05
6.2e-05
5.9e-05
5.1e-05
4.9e-05
4.3e-05
4.2e-05
3.5e-05
3.6e-05
3.2e-05
3e-05
2.7e-05
2.6e-05
2.4e-05
2.1e-05
2e-05
1.8e-05
1.7e-05
1.6e-05
1.4e-05
1.3e-05
1.2e-05
1.2e-05
1.1e-05
1e-05
9.2e-06
8.6e-06
8.4e-06
7.6e-06
7e-06
6.8e-06
6.2e-06
6e-06
5.4e-06
5e-06
4.8e-06
4.5e-06
4.3e-06
4e-06
3.8e-06
3.7e-06
3.5e-06
3.4e-06
3.1e-06
3e-06
2.9e-06
2.8e-06
2.6e-06
2.5e-06
2.4e-06
2.3e-06
2.2e-06
2.1e-06
2e-06
1.9e-06
1.9e-06
1.8e-06
1.8e-06
1.7e-06
1.7e-06
1.7e-06
1.6e-06
1.5e-06
1.6e-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
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
wsum_model.pdf_direction[exp_ipart]=
0
mymodel.avg_norm_correction= 0.747016
wsum_model.avg_norm_correction= 0
written out Mweight.spi
exp_thisparticle_sumweight= -nan
exp_min_diff2[exp_ipart]= 5.61233
slave 14 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
====== Initiaisation =====
--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 soflisation =====
--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 solisation =====
--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 sosation =====
--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--------------------------------------------------------------------------
mpirun has exited due to process rank 5 with PID 31431 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:31424] 10 more processes have sent help message help-mpi-api.txt / mpi-abort
[knoll:31424] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
isation =====
--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 sofisation =====
--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 sofalisation =====
--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 sisation =====
--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
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
t 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
Does anyone have suggestions to fix this? Thanks for your help.
Sincerely,
Ali Khan
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