protomo2aligner.py --parallel=True --starting_tlt_file=My_tlt_file --negative=-44 --r1_region_x=2878 --r2_region_x=2878 --r3_region_x=2878 --r4_region_x=2878 --r5_region_x=2878 --r1_region_y=2782 --r2_region_y=2782 --r3_region_y=2782 --r4_region_y=2782 --r5_region_y=2782 --r1_sampling=2 --r2_sampling=1 --r3_sampling=1 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=1500 --r1_mask_width_x=1414 --r2_mask_width_x=2853 --r3_mask_width_x=2853 --r4_mask_width_x=2853 --r5_mask_width_x=2853 --r1_mask_width_y=1366 --r2_mask_width_y=2757 --r3_mask_width_y=2757 --r4_mask_width_y=2757 --r5_mask_width_y=2757 --r1_lowpass_diameter_x=12.5 --r2_lowpass_diameter_x=6.25 --r3_lowpass_diameter_x=3.125 --r4_lowpass_diameter_x=3.125 --r5_lowpass_diameter_x=3.125 --r1_lowpass_diameter_y=12.5 --r2_lowpass_diameter_y=6.25 --r3_lowpass_diameter_y=3.125 --r4_lowpass_diameter_y=3.125 --r5_lowpass_diameter_y=3.125 --r1_highpass_diameter_x=5107 --r2_highpass_diameter_x=5107 --r3_highpass_diameter_x=5107 --r4_highpass_diameter_x=5107 --r5_highpass_diameter_x=5107 --r1_highpass_diameter_y=5107 --r2_highpass_diameter_y=5107 --r3_highpass_diameter_y=5107 --r4_highpass_diameter_y=5107 --r5_highpass_diameter_y=5107 --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 --r5_mask_apod_y=10 --r1_lowpass_apod_x=31 --r2_lowpass_apod_x=16 --r3_lowpass_apod_x=8 --r4_lowpass_apod_x=8 --r5_lowpass_apod_x=8 --r1_lowpass_apod_y=31 --r2_lowpass_apod_y=16 --r3_lowpass_apod_y=8 --r4_lowpass_apod_y=8 --r5_lowpass_apod_y=8 --r1_highpass_apod_x=2554 --r2_highpass_apod_x=2554 --r3_highpass_apod_x=2554 --r4_highpass_apod_x=2554 --r5_highpass_apod_x=2554 --r1_highpass_apod_y=2554 --r2_highpass_apod_y=2554 --r3_highpass_apod_y=2554 --r4_highpass_apod_y=2554 --r5_highpass_apod_y=2554 --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf --r5_corr_mode=pcf --r1_iters=15 --r2_iters=10 --r3_iters=0 --r4_iters=0 --r5_iters=0 --preprocessing=true --exclude_images_by_angle_accuracy=0.05 --border=100 --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false --filter=median --r1_kernel_x=5 --r2_kernel_x=5 --r3_kernel_x=5 --r4_kernel_x=5 --r5_kernel_x=5 --r1_kernel_y=5 --r2_kernel_y=5 --r3_kernel_y=5 --r4_kernel_y=5 --r5_kernel_y=5 --grow=0 --window_area=0.95 --do_estimation=false --norotations=false --correlation_size_x=160 --correlation_size_y=160 --r1_peak_search_radius_x=300 --r2_peak_search_radius_x=300 --r3_peak_search_radius_x=300 --r4_peak_search_radius_x=300 --r5_peak_search_radius_x=300 --r1_peak_search_radius_y=300 --r2_peak_search_radius_y=300 --r3_peak_search_radius_y=300 --r4_peak_search_radius_y=300 --r5_peak_search_radius_y=300 --translimit=1000 --orientation=true --azimuth=true --elevation=false --rotation=true --scale=false --scale_switch=31 --logging=true --loglevel=2 --create_tilt_video=true --create_reconstruction=true --show_window_size=true --keep_recons=false --slab=true --map_size_x=479 --map_size_y=463 --tilt_clip=true --video_type=html5vid --runname=tiltseries0048dc --rundir=/gpfs/appion/jbrasch/17feb10h/protomo_alignments/tiltseries0048dc --tiltseries=48 --sessionname=17feb10h --pixelsize=1.83586 --dimx=3838 --dimy=3710 --image_file_type=mrc --coarse=False --projectid=282 --expid=3450 --jobtype=protomo node07 Start time: 2017yr03m10d-16hr48m06s Description: Using user-provided tlt file series0048.tlt for Refinement.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #48 lowpass = 12.5 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 2, pixelsize is 3.67172 Angstroms, Nyquist is 7.34344 Angstroms) window.lowpass.apodization = { 0.23688516129 0.23688516129 } map.sampling = 2 window.highpass.diameter = { 0.00143791658508 0.00143791658508 } window.highpass.apodization = { 0.00287527016445 0.00287527016445 } window.mask.apodization = { 10 10 } align.mask.width = { 1414 1366 } sampling = 2 align.mask.apodization = { 10 10 } map.body = 694.945679823 map.lowpass.diameter = { 0.5874752 0.5874752 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 1439 1391 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 1414 1366 } reference.body = 694.945679823 window.lowpass.diameter = { 0.5874752 0.5874752 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Creating quality assessment statistics... CCMS(shift) = 0.01376 for Iteration #1 of Tilt-Series #48. CCMS(rotations) = 0.51865 for Iteration #1 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #48. The scaled sum of CCMS values is #0.01726 for Tilt-Series #48. Creating Depiction Videos for Iteration #1 in Parallel... Creating Refinement tilt-series video for iteration #1... Generating Refinement reconstruction for iteration #1... No Round parameters changed for Iteration #2 of Tilt-Series #48 Beginning Refinement Iteration #2, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #2 Creating quality assessment statistics... CCMS(shift) = 0.01254 for Iteration #2 of Tilt-Series #48. CCMS(rotations) = 0.33685 for Iteration #2 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #48. The scaled sum of CCMS values is #0.01301 for Tilt-Series #48. Creating Depiction Videos for Iteration #2 in Parallel... Creating Refinement tilt-series video for iteration #2... Generating Refinement reconstruction for iteration #2... No Round parameters changed for Iteration #3 of Tilt-Series #48 Beginning Refinement Iteration #3, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #3 Creating quality assessment statistics... CCMS(shift) = 0.00884 for Iteration #3 of Tilt-Series #48. CCMS(rotations) = 0.40591 for Iteration #3 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #48. The scaled sum of CCMS values is #0.01254 for Tilt-Series #48. Creating Depiction Videos for Iteration #3 in Parallel... Creating Refinement tilt-series video for iteration #3... Generating Refinement reconstruction for iteration #3... No Round parameters changed for Iteration #4 of Tilt-Series #48 Beginning Refinement Iteration #4, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #4 Creating quality assessment statistics... CCMS(shift) = 0.00917 for Iteration #4 of Tilt-Series #48. CCMS(rotations) = 0.35369 for Iteration #4 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #4 of Tilt-Series #48. The scaled sum of CCMS values is #0.01166 for Tilt-Series #48. Creating Depiction Videos for Iteration #4 in Parallel... Creating Refinement tilt-series video for iteration #4... Generating Refinement reconstruction for iteration #4... No Round parameters changed for Iteration #5 of Tilt-Series #48 Beginning Refinement Iteration #5, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #5 Creating quality assessment statistics... CCMS(shift) = 0.01301 for Iteration #5 of Tilt-Series #48. CCMS(rotations) = 0.34437 for Iteration #5 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #5 of Tilt-Series #48. The scaled sum of CCMS values is #0.01339 for Tilt-Series #48. Creating Depiction Videos for Iteration #5 in Parallel... Creating Refinement tilt-series video for iteration #5... Generating Refinement reconstruction for iteration #5... No Round parameters changed for Iteration #6 of Tilt-Series #48 Beginning Refinement Iteration #6, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #6 Creating quality assessment statistics... CCMS(shift) = 0.00951 for Iteration #6 of Tilt-Series #48. CCMS(rotations) = 0.25721 for Iteration #6 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #6 of Tilt-Series #48. The scaled sum of CCMS values is #0.0099 for Tilt-Series #48. Creating Depiction Videos for Iteration #6 in Parallel... Creating Refinement tilt-series video for iteration #6... Generating Refinement reconstruction for iteration #6... No Round parameters changed for Iteration #7 of Tilt-Series #48 Beginning Refinement Iteration #7, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #7 Creating quality assessment statistics... CCMS(shift) = 0.0137 for Iteration #7 of Tilt-Series #48. CCMS(rotations) = 0.50171 for Iteration #7 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #7 of Tilt-Series #48. The scaled sum of CCMS values is #0.01688 for Tilt-Series #48. Creating Depiction Videos for Iteration #7 in Parallel... Creating Refinement tilt-series video for iteration #7... Generating Refinement reconstruction for iteration #7... No Round parameters changed for Iteration #8 of Tilt-Series #48 Beginning Refinement Iteration #8, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #8 Creating quality assessment statistics... CCMS(shift) = 0.0102 for Iteration #8 of Tilt-Series #48. CCMS(rotations) = 0.31217 for Iteration #8 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #8 of Tilt-Series #48. The scaled sum of CCMS values is #0.01134 for Tilt-Series #48. Creating Depiction Videos for Iteration #8 in Parallel... Creating Refinement tilt-series video for iteration #8... Generating Refinement reconstruction for iteration #8... No Round parameters changed for Iteration #9 of Tilt-Series #48 Beginning Refinement Iteration #9, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #9 Creating quality assessment statistics... CCMS(shift) = 0.01114 for Iteration #9 of Tilt-Series #48. CCMS(rotations) = 0.4381 for Iteration #9 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #9 of Tilt-Series #48. The scaled sum of CCMS values is #0.01433 for Tilt-Series #48. Creating Depiction Videos for Iteration #9 in Parallel... Creating Refinement tilt-series video for iteration #9... Generating Refinement reconstruction for iteration #9... No Round parameters changed for Iteration #10 of Tilt-Series #48 Beginning Refinement Iteration #10, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #10 Creating quality assessment statistics... CCMS(shift) = 0.00906 for Iteration #10 of Tilt-Series #48. CCMS(rotations) = 0.41618 for Iteration #10 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #10 of Tilt-Series #48. The scaled sum of CCMS values is #0.01286 for Tilt-Series #48. Creating Depiction Videos for Iteration #10 in Parallel... Creating Refinement tilt-series video for iteration #10... Generating Refinement reconstruction for iteration #10... No Round parameters changed for Iteration #11 of Tilt-Series #48 Beginning Refinement Iteration #11, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #11 Creating quality assessment statistics... CCMS(shift) = 0.01048 for Iteration #11 of Tilt-Series #48. CCMS(rotations) = 0.43652 for Iteration #11 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #11 of Tilt-Series #48. The scaled sum of CCMS values is #0.01397 for Tilt-Series #48. Creating Depiction Videos for Iteration #11 in Parallel... Creating Refinement tilt-series video for iteration #11... Generating Refinement reconstruction for iteration #11... No Round parameters changed for Iteration #12 of Tilt-Series #48 Beginning Refinement Iteration #12, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #12 Creating quality assessment statistics... CCMS(shift) = 0.00903 for Iteration #12 of Tilt-Series #48. CCMS(rotations) = 0.31988 for Iteration #12 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #12 of Tilt-Series #48. The scaled sum of CCMS values is #0.01091 for Tilt-Series #48. Creating Depiction Videos for Iteration #12 in Parallel... Creating Refinement tilt-series video for iteration #12... Generating Refinement reconstruction for iteration #12... No Round parameters changed for Iteration #13 of Tilt-Series #48 Beginning Refinement Iteration #13, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #13 Creating quality assessment statistics... CCMS(shift) = 0.01072 for Iteration #13 of Tilt-Series #48. CCMS(rotations) = 0.40664 for Iteration #13 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #13 of Tilt-Series #48. The scaled sum of CCMS values is #0.01349 for Tilt-Series #48. Creating Depiction Videos for Iteration #13 in Parallel... Creating Refinement tilt-series video for iteration #13... Generating Refinement reconstruction for iteration #13... No Round parameters changed for Iteration #14 of Tilt-Series #48 Beginning Refinement Iteration #14, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #14 Creating quality assessment statistics... CCMS(shift) = 0.00878 for Iteration #14 of Tilt-Series #48. CCMS(rotations) = 0.28505 for Iteration #14 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #14 of Tilt-Series #48. The scaled sum of CCMS values is #0.01009 for Tilt-Series #48. Creating Depiction Videos for Iteration #14 in Parallel... Creating Refinement tilt-series video for iteration #14... Generating Refinement reconstruction for iteration #14... No Round parameters changed for Iteration #15 of Tilt-Series #48 Beginning Refinement Iteration #15, Round #1 of Tilt-Series #48 No parameters were switched for Iteration #15 Creating quality assessment statistics... CCMS(shift) = 0.00744 for Iteration #15 of Tilt-Series #48. CCMS(rotations) = 0.27849 for Iteration #15 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #15 of Tilt-Series #48. The scaled sum of CCMS values is #0.00929 for Tilt-Series #48. Creating Depiction Videos for Iteration #15 in Parallel... Creating Refinement tilt-series video for iteration #15... Generating Refinement reconstruction for iteration #15... Beginning Refinement Iteration #16, Round #2 of Tilt-Series #48 lowpass = 6.25 angstroms Round #2. Parameters in Protomo units: (Note: At binned by 1, pixelsize is 1.83586 Angstroms, Nyquist is 3.67172 Angstroms) window.lowpass.apodization = { 0.2294825 0.2294825 } map.sampling = 1 window.highpass.diameter = { 0.00071895829254 0.00071895829254 } window.highpass.apodization = { 0.00143763508222 0.00143763508222 } window.mask.apodization = { 10 10 } align.mask.width = { 2853 2757 } sampling = 1 align.mask.apodization = { 10 10 } map.body = 1389.89135965 map.lowpass.diameter = { 0.5874752 0.5874752 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 2878 2782 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 2853 2757 } reference.body = 1389.89135965 window.lowpass.diameter = { 0.5874752 0.5874752 } align.correlation.mode = mcf No parameters were switched for Iteration #16 Creating quality assessment statistics... CCMS(shift) = 0.00728 for Iteration #16 of Tilt-Series #48. CCMS(rotations) = 0.31774 for Iteration #16 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #16 of Tilt-Series #48. The scaled sum of CCMS values is #0.01 for Tilt-Series #48. Creating Depiction Videos for Iteration #16 in Parallel... Creating Refinement tilt-series video for iteration #16... Generating Refinement reconstruction for iteration #16... No Round parameters changed for Iteration #17 of Tilt-Series #48 Beginning Refinement Iteration #17, Round #2 of Tilt-Series #48 No parameters were switched for Iteration #17 Creating quality assessment statistics... CCMS(shift) = 0.01477 for Iteration #17 of Tilt-Series #48. CCMS(rotations) = 0.53836 for Iteration #17 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #17 of Tilt-Series #48. The scaled sum of CCMS values is #0.01815 for Tilt-Series #48. Creating Depiction Videos for Iteration #17 in Parallel... Creating Refinement tilt-series video for iteration #17... Generating Refinement reconstruction for iteration #17... No Round parameters changed for Iteration #18 of Tilt-Series #48 Beginning Refinement Iteration #18, Round #2 of Tilt-Series #48 No parameters were switched for Iteration #18 Creating quality assessment statistics... CCMS(shift) = 0.01411 for Iteration #18 of Tilt-Series #48. CCMS(rotations) = 0.53189 for Iteration #18 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #18 of Tilt-Series #48. The scaled sum of CCMS values is #0.01769 for Tilt-Series #48. Creating Depiction Videos for Iteration #18 in Parallel... Creating Refinement tilt-series video for iteration #18... Generating Refinement reconstruction for iteration #18... No Round parameters changed for Iteration #19 of Tilt-Series #48 Beginning Refinement Iteration #19, Round #2 of Tilt-Series #48 No parameters were switched for Iteration #19 Creating quality assessment statistics... CCMS(shift) = 0.01472 for Iteration #19 of Tilt-Series #48. CCMS(rotations) = 0.51088 for Iteration #19 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #19 of Tilt-Series #48. The scaled sum of CCMS values is #0.01758 for Tilt-Series #48. Creating Depiction Videos for Iteration #19 in Parallel... Creating Refinement tilt-series video for iteration #19... Generating Refinement reconstruction for iteration #19... No Round parameters changed for Iteration #20 of Tilt-Series #48 Beginning Refinement Iteration #20, Round #2 of Tilt-Series #48 No parameters were switched for Iteration #20 Creating quality assessment statistics... CCMS(shift) = 0.01515 for Iteration #20 of Tilt-Series #48. CCMS(rotations) = 0.51344 for Iteration #20 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #20 of Tilt-Series #48. The scaled sum of CCMS values is #0.01784 for Tilt-Series #48. Creating Depiction Videos for Iteration #20 in Parallel... Creating Refinement tilt-series video for iteration #20... Generating Refinement reconstruction for iteration #20... No Round parameters changed for Iteration #21 of Tilt-Series #48 Beginning Refinement Iteration #21, Round #2 of Tilt-Series #48 No parameters were switched for Iteration #21 Creating quality assessment statistics... CCMS(shift) = 0.0165 for Iteration #21 of Tilt-Series #48. CCMS(rotations) = 0.61453 for Iteration #21 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #21 of Tilt-Series #48. The scaled sum of CCMS values is #0.02054 for Tilt-Series #48. Creating Depiction Videos for Iteration #21 in Parallel... Creating Refinement tilt-series video for iteration #21... Generating Refinement reconstruction for iteration #21... No Round parameters changed for Iteration #22 of Tilt-Series #48 Beginning Refinement Iteration #22, Round #2 of Tilt-Series #48 No parameters were switched for Iteration #22 Creating quality assessment statistics... CCMS(shift) = 0.01439 for Iteration #22 of Tilt-Series #48. CCMS(rotations) = 0.54938 for Iteration #22 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #22 of Tilt-Series #48. The scaled sum of CCMS values is #0.01818 for Tilt-Series #48. Creating Depiction Videos for Iteration #22 in Parallel... Creating Refinement tilt-series video for iteration #22... Generating Refinement reconstruction for iteration #22... No Round parameters changed for Iteration #23 of Tilt-Series #48 Beginning Refinement Iteration #23, Round #2 of Tilt-Series #48 No parameters were switched for Iteration #23 Creating quality assessment statistics... CCMS(shift) = 0.01353 for Iteration #23 of Tilt-Series #48. CCMS(rotations) = 0.51994 for Iteration #23 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #23 of Tilt-Series #48. The scaled sum of CCMS values is #0.01716 for Tilt-Series #48. Creating Depiction Videos for Iteration #23 in Parallel... Creating Refinement tilt-series video for iteration #23... Generating Refinement reconstruction for iteration #23... No Round parameters changed for Iteration #24 of Tilt-Series #48 Beginning Refinement Iteration #24, Round #2 of Tilt-Series #48 No parameters were switched for Iteration #24 Creating quality assessment statistics... CCMS(shift) = 0.01559 for Iteration #24 of Tilt-Series #48. CCMS(rotations) = 0.62356 for Iteration #24 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #24 of Tilt-Series #48. The scaled sum of CCMS values is #0.02027 for Tilt-Series #48. Creating Depiction Videos for Iteration #24 in Parallel... Creating Refinement tilt-series video for iteration #24... Generating Refinement reconstruction for iteration #24... No Round parameters changed for Iteration #25 of Tilt-Series #48 Beginning Refinement Iteration #25, Round #2 of Tilt-Series #48 No parameters were switched for Iteration #25 Creating quality assessment statistics... CCMS(shift) = 0.0151 for Iteration #25 of Tilt-Series #48. CCMS(rotations) = 0.56221 for Iteration #25 of Tilt-Series #48. CCMS(scale) = 0.0 for Iteration #25 of Tilt-Series #48. The scaled sum of CCMS values is #0.0188 for Tilt-Series #48. Creating Depiction Videos for Iteration #25 in Parallel... Creating Refinement tilt-series video for iteration #25... Generating Refinement reconstruction for iteration #25... Finished Refinement for Tilt-Series #48! Did everything blow up and now you're yelling at your computer screen? If so, kindly email Alex at anoble@nysbc.org and include this log file .If everything worked beautifully and you publish it, please use the appropriate citations listed on the Appion webpage! You can also print out all citations by typing: protomo2aligner.py --citations End time: 2017yr03m12d-15hr36m19s