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
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