We do not seem to be running out of RAM. I check as RAM usage as it is running, and it does not come anywhere near the maximum of the machine.
I have this problem with both my images and the tutorial images.
Sent from my iPhone
> On Dec 11, 2014, at 2:26 PM, Sjors Scheres <[log in to unmask]> wrote:
>
> 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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