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Subject:

Re: Relion 1.3: Can't use multiple MPI proc

From:

Sjors Scheres <[log in to unmask]>

Reply-To:

Sjors Scheres <[log in to unmask]>

Date:

Thu, 11 Dec 2014 19:26:41 -0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (10112 lines)

Hmm, hard to tell. Are these your own images? To exclude the possibility
you did something wrong with the preprocessing, perhaps you could try the
data from the tutorial. Also, do make sure you are not running out of RAM
when running multiple MPI processes on a single computer.
HTH,
S
> Dr. Scheres,
>
> I tried using the relion 1.3 tutorial data, and I get the same issue in 2D
> classification when MPI process is >1. Output is below:
>
> Executing: mpirun -n 6 `which relion_refine_mpi` --o Class2D/autopick_sort
> --i particles_autopick_sort.star --particle_diameter 200 --angpix 1 --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 1  &
>  === RELION MPI setup ===
>  + Number of MPI processes             = 6
>  + Number of threads per MPI process  = 2
>  + Total number of threads therefore  = 12
>  + Master  (0) runs on host            = mycomputer
>  =================
>  + Slave     1 runs on host            = mycomputer
>  + Slave     2 runs on host            = mycomputer
>  + Slave     3 runs on host            = mycomputer
>  + Slave     4 runs on host            = mycomputer
>  + Slave     5 runs on host            = mycomputer
> MlOptimiser::initialiseGeneral: WARNING modifying pixel size from 1 to
> 3.54
> based on magnification information in the input STAR file
>  Estimating initial noise spectra
> 000/??? sec
> ~~(,_,">                                                          [o   4/
> 4 sec ...........................................................~~(,_,"
> 4/   4 sec
> ............................................................~~(,_,">
>  Estimating accuracies in the orientational assignment ...
> 000/??? sec
> ~~(,_,">                                                          [o  36/
> 36 sec ...........................................................~~(,_,"
> 36/  36 sec
> ...........................................................~~(,_,"  36/
> 36
> sec ...........................................................~~(,_,"
> 36/  36 sec
> ...........................................................~~(,_,"  36/
> 36
> sec ...........................................................~~(,_,"
> 36/  36 sec
> ...........................................................~~(,_,"  36/
> 36
> sec ...........................................................~~(,_,"
> 36/  36 sec
> ...........................................................~~(,_,"  37/
> 37
> sec ...........................................................~~(,_,"
> 37/  37 sec
> ...........................................................~~(,_,"  37/
> 37
> sec ...........................................................~~(,_,"
> 37/  37 sec
> ...........................................................~~(,_,"  37/
> 37
> sec ...........................................................~~(,_,"
> 37/  37 sec
> ...........................................................~~(,_,"  37/
> 37
> sec ...........................................................~~(,_,"
> 37/  37 sec
> ...........................................................~~(,_,"  37/
> 37
> sec ............................................................~~(,_,">
>  Auto-refine: Estimated accuracy angles= 30.1 degrees; offsets= 4.25
> 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= 49.088 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  > 0.262636 Gb, available memory =
> 2
> Gb.
>  Estimated memory for maximization step > 0.000331923 Gb, available memory
> = 2 Gb.
>  Expectation iteration 1 of 25
> 000/??? sec
> ~~(,_,">
> [o5.25/5.30 min
> ...........................................................~~(,_,"5.32/5.30
> min
> ............................................................~~(,_,5.33/5.33
> min ............................................................~~(,_,">
>  Maximization ...
> 000/??? sec
> ~~(,_,">                                                          [o   1/
> 1 sec ............................................................~~(,_,">
>  Estimating accuracies in the orientational assignment ...
> 000/??? sec
> ~~(,_,">                                                          [o   8/
> 8 sec ............................................................~~(,_,">
>  Auto-refine: Estimated accuracy angles= 30.1 degrees; offsets= 2.11
> 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= 147.264 Angstroms, which requires orientationSampling
> of at least 72 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 =
> 2
> Gb.
>  Estimated memory for maximization step > 0.000135183 Gb, available memory
> = 2 Gb.
>  Expectation iteration 2 of 25
> 000/??? sec
> ~~(,_,">                                                          [oo]
> exp_thisparticle_sumweight= -nan
>  exp_thisparticle_sumweight= -nan
>  exp_part_id= 1538exp_iimage=1
>  group_id= 2 mymodel.scale_correction[group_id]= 1.06665
>  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]=
>    0.00038
>    5.3e-06
>    4.8e-06
>    4.8e-06
>    5.9e-06
>    7.7e-06
>    9.5e-06
>    1.1e-05
>    1.1e-05
>    1.1e-05
>    1.1e-05
>      1e-05
>    9.2e-06
>    8.2e-06
>    7.5e-06
>    7.4e-06
>    7.5e-06
>    7.5e-06
>      7e-06
>    6.3e-06
>    5.5e-06
>    4.7e-06
>    3.9e-06
>    3.3e-06
>    2.6e-06
>    2.4e-06
>    2.1e-06
>    1.9e-06
>    1.8e-06
>    1.7e-06
>    1.8e-06
>    1.8e-06
>    1.9e-06
>    1.9e-06
>    1.9e-06
>    1.8e-06
>    1.7e-06
>    1.6e-06
>    1.5e-06
>    1.4e-06
>    1.3e-06
>    1.3e-06
>    1.3e-06
>    1.3e-06
>    1.3e-06
>    1.3e-06
>    1.2e-06
>    1.1e-06
>      1e-06
>    9.9e-07
>    9.8e-07
>    9.9e-07
>    9.8e-07
>    9.5e-07
>    9.1e-07
>    8.5e-07
>    8.1e-07
>    7.9e-07
>    7.8e-07
>    7.7e-07
>    7.5e-07
>    7.2e-07
>    6.8e-07
>    6.6e-07
>    6.4e-07
>    6.4e-07
>    6.3e-07
>    6.1e-07
>    5.8e-07
>    5.5e-07
>    5.4e-07
>    5.3e-07
>    5.2e-07
>      5e-07
>    4.8e-07
>    4.7e-07
>    4.6e-07
>    4.6e-07
>    4.4e-07
>    4.2e-07
>    4.1e-07
>      4e-07
>      4e-07
>    3.9e-07
>    3.7e-07
>    3.6e-07
>    3.5e-07
>    3.5e-07
>    3.4e-07
>    3.3e-07
>    3.2e-07
>    3.2e-07
>    3.1e-07
>      3e-07
>      3e-07
>    2.9e-07
>    2.8e-07
>    2.8e-07
>    2.7e-07
>    2.6e-07
>    2.6e-07
>    2.6e-07
>    2.5e-07
>    2.5e-07
>    2.5e-07
>
>  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
>          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= 0.259929
>  wsum_model.avg_norm_correction= 0
> written out Mweight.spi
>  exp_thisparticle_sumweight= -nan
>  exp_min_diff2[exp_ipart]= 56.8061
> 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
> --------------------------------------------------------------------------
> 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= 1406exp_iimage=1
>  group_id= 2 mymodel.scale_correction[group_id]= 1.06665
>  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]=
>    0.00038
>    5.3e-06
>    4.8e-06
>    4.8e-06
>    5.9e-06
>    7.7e-06
>    9.5e-06
>    1.1e-05
>    1.1e-05
>    1.1e-05
>    1.1e-05
>      1e-05
>    9.2e-06
>    8.2e-06
>    7.5e-06
>    7.4e-06
>    7.5e-06
>    7.5e-06
>      7e-06
>    6.3e-06
>    5.5e-06
>    4.7e-06
>    3.9e-06
>    3.3e-06
>    2.6e-06
>    2.4e-06
>    2.1e-06
>    1.9e-06
>    1.8e-06
>    1.7e-06
>    1.8e-06
>    1.8e-06
>    1.9e-06
>    1.9e-06
>    1.9e-06
>    1.8e-06
>    1.7e-06
>    1.6e-06
>    1.5e-06
>    1.4e-06
>    1.3e-06
>    1.3e-06
>    1.3e-06
>    1.3e-06
>    1.3e-06
>    1.3e-06
>    1.2e-06
>    1.1e-06
>      1e-06
>    9.9e-07
>    9.8e-07
>    9.9e-07
>    9.8e-07
>    9.5e-07
>    9.1e-07
>    8.5e-07
>    8.1e-07
>    7.9e-07
>    7.8e-07
>    7.7e-07
>    7.5e-07
>    7.2e-07
>    6.8e-07
>    6.6e-07
>    6.4e-07
>    6.4e-07
>    6.3e-07
>    6.1e-07
>    5.8e-07
>    5.5e-07
>    5.4e-07
>    5.3e-07
>    5.2e-07
>      5e-07
>    4.8e-07
>    4.7e-07
>    4.6e-07
>    4.6e-07
>    4.4e-07
>    4.2e-07
>    4.1e-07
>      4e-07
>      4e-07
>    3.9e-07
>    3.7e-07
>    3.6e-07
>    3.5e-07
>    3.5e-07
>    3.4e-07
>    3.3e-07
>    3.2e-07
>    3.2e-07
>    3.1e-07
>      3e-07
>      3e-07
>    2.9e-07
>    2.8e-07
>    2.8e-07
>    2.7e-07
>    2.6e-07
>    2.6e-07
>    2.6e-07
>    2.5e-07
>    2.5e-07
>    2.5e-07
>
>  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
>          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= 0.259929
>  wsum_model.avg_norm_correction= 0
> written out Mweight.spi
>  exp_thisparticle_sumweight= -nan
>  exp_min_diff2[exp_ipart]= 56.8061
> 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
>                            --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
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 5 with PID 16537 on
> node mycomputer 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).
> --------------------------------------------------------------------------
> [mycomputer:16530] 1 more process has sent help message help-mpi-api.txt /
> mpi-abort
> [mycomputer:16530] Set MCA parameter "orte_base_help_aggregate" to 0 to
> see
> all help / error messages
>
>
>
> On Tue, Dec 9, 2014 at 3:40 PM, Sjors Scheres <[log in to unmask]>
> wrote:
>
>> Hi Ali,
>> It seems that MPI is running OK (using 30 processes all on knoll; was
>> that
>> your intention?). The errors may be due to the warnings you get: your
>> groups are very small. Try making those larger as suggested (and as
>> explained in the tutorial).
>> HTH,
>> S
>>
>> > 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]=
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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]= 15.2914
>> >  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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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]= 17.8113
>> >  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]=
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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]= 17.4846
>> >  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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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]= 14.9149
>> >  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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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]= 17.4735
>> > 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]=
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >      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]=
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >       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]=
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >       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]=
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >      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
>> >    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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >       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
>> >    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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >     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
>> >    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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >       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
>> >    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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >       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
>> >    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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >       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]=
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >       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]=
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >      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]=
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          0
>> >          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]= 17.3356
>> > 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
>> >
>>
>>
>> --
>> Sjors Scheres
>> MRC Laboratory of Molecular Biology
>> Francis Crick Avenue, Cambridge Biomedical Campus
>> Cambridge CB2 0QH, U.K.
>> tel: +44 (0)1223 267061
>> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>>
>>
>


-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres

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