set inventory_do = "0"
set inventory_image_do = "0"
set test_spacegroups_doit = "y"
set test_spacegroups_val = "ALL"
set export_already_done = "n"
set show_frames = "n"
set show_frame_FFT = "n"
set show_frame_CCmap = "n"
set show_frame_PROFDATA = "n"
set show_frame_CCmap_marked = "n"
set show_frame_CCmap_unbent = "n"
set show_hkl = "n"
set show_phares = "n"
set show_PSF = "n"
set eval_lattice_doswap = "0"
set eval_lattice_do1 = "0"
set eval_lattice_do2 = "0"
set eval_lattice_do3 = "0"
set eval_lattice_do4 = "0"
set eval_lattice_dorotate = "0"
# LOCKED: YES
set eval_lattice_overwriteRealLattice = "n"
set eval_lattice_overwriteTiltgeometry = "n"
set eval_lattice_regenPL = "n"
set eval_lattice_peakNum = "140"
set MASKING_done = "y"
set refine_maska_doit_1 = "y"
set refine_boxa1_doit_1 = "y"
set refine_maska_boxa1_doit = "n"
set refine_maska_doit_2 = "n"
set refine_boxa1_doit_2 = "n"
set refine_maska_doit_3 = "n"
set refine_boxa1_doit_3 = "n"
set refine_maskb01_doit_1 = "y"
set refine_boxb1_doit_1 = "y"
set refine_maskb01_boxb1_doit = "n"
set refine_maskb02_doit_1 = "n"
set refine_maskb01_doit_2 = "n"
set refine_boxb1_doit_2 = "n"
set refine_maskb01_doit_3 = "n"
set refine_boxb1_doit_3 = "n"
# ISWRONG: YES
set specimen_name = "-"
# ISWRONG: YES
set specimennumber = "-"
# ISWRONG: YES
set tomo_series_number = "-"
set imagenumber = "0000012800"
set imagename = "mauto_45"
set nonmaskimagename = "auto_45"
set image_evenodd = "2"
set comment = "-"
# ISWRONG: YES
set image_flag = "none"
set imagesidelength = "3808"
set magnification = "37313.4"
# LOCKED: YES
set stepdigitizer = "5"
set sample_pixel = "1.34"
set take_header_orig_sample_pixel = "y"
set orig_sample_pixel = "1.0"
# ISWRONG: YES
set iciness = "-"
set iciness2 = "-"
set imagename_original = "2014-07-02_12.48.24_aligned.mrc"
# ISWRONG: YES
set specimen_recording_day = "-"
# ISWRONG: YES
set specimen_recording_time = "-"
set last_processed = "19.09.2017 18:11"
# ISWRONG: YES
set new_imagenumber = "PutUniqueNumberHere"
set doswap = "0"
set import_rawstack = "PutNameHere"
set import_rawstack_original = "PutNameHere"
set import_original_time = "-"
set raw_gaincorrectedstack = "PutNameHere"
set raw_gaincorrectedstack_original = "PutNameHere"
set import_defects = ""
set import_defects_original = ""
set import_gainref = "../Counted_gainref.dm4"
set import_gainref_original = ""
set SERIALEM_FACTOR = "1"
set SERIALEM_DEFAULT_FACTOR = "12"
set import_drift = "."
set import_drift_longest = "."
set import_drift_deceleration = "."
set import_drift_jitter = "."
set prior_dose = "."
set frame_image_counts = "."
set frame_image_dose = "."
set frame_dose = "."
set total_dose = "."
set movie_enable = "n"
set movie_inmovie = "n"
# ISWRONG: YES
set movie_stackname_raw = "ScriptWillPutNameHere"
set movie_stackname = "movie_aligned"
set movie_imagenumber_total = "ScriptWillPutNumberHere"
set movie_imagenumber_black = "ScriptWillPutNumberHere"
set movie_imagenumber_toave = "7"
set movie_imagenumber_toskip = "0"
set movie_imagenumber_touse = "ScriptWillPutNumberHere"
set movie_masking_mode = "1"
set movie_refboxa = "300"
set movie_refboxb = "0"
# ISWRONG: YES
set movie_quadrada = "3,3"
set movie_quadradb = "8,8"
# LOCKED: YES
# ISWRONG: YES
set movie_facthreshb = "0.05"
set movie_filter_type = "0"
# LOCKED: YES
set movie_filter_param = "1.0,-0.03648"
# ISWRONG: YES
set movie_stack_folder = "~/data/2dx/project/stacks"
set movie_smoothing = "8"
set movie_drift_threshold = "5"
set generatePeriodogram = "y"
set defocus_direction = "0"
set det_defocus = "y"
set defocus = "15835.22,15210.35,-80.71"
set defocusbackup = "15681.75,16086.29,0.01"
# ISWRONG: YES
set expected_tltang = "0.0"
# ISWRONG: YES
set expected_tltang_uncertainty = "60.0"
set defocus_RESMAX = "."
set gctf_RESMAX = "."
set CTFFIND4_RESMAX = "."
set gctf_CCvalue = "."
set CTFFIND4_CCvalue = "."
set defocus_CCvalue = "."
set CTFFIND4_phase_shift = "."
set gCTF_phase_shift = "."
set defocus_phase_shift = "."
set gctf_defocus = "."
set CTFFIND4_defocus = "."
set defocus_defocus = "."
set TLTAXIS = "89.503"
set TLTANG = "-26.1952664537"
set TLTAXA = "66.977"
set TAXA = "66.783"
set TANGL = "26.1952664537"
set TAXA_change = "-0.421"
set TANGL_change = "0.443"
set beamtilt = "0.0,0.0"
set beamtilt_magnitude = "4.915"
set beamtilt_change = "-1.031,0.444"
set LATTICE_done = "y"
set laterror_abserror = "62.256"
set laterror_rmsderror = "1.48975"
set laterror_peaksused = "140 of 140"
set laterror_nodepeakdensity = "1.30354"
set realcell_local = "133.578, 134.357"
set realang_local = "89.801"
# LOCKED: YES
set regenPL = "y"
set lattice = "38.989,-15.338,17.403,34.933"
set secondlattice = "-0,0.0,-0,0.0"
# ISWRONG: YES
set secondlattice_exists = "n"
# ISWRONG: YES
set secondlattice_is_this = "n"
set backuplattice = "0.0,0.0,0.0,0.0"
set flag_lefthanded_lattice = "n"
# LOCKED: YES
set ProtSpotList = "n"
set treatspotscan = "n"
set quadrada = "9,9"
set quadradb = "8,8"
# ISWRONG: YES
set SYN_quadrada = "9,9"
# ISWRONG: YES
set SYN_quadradb = "8,8"
# LOCKED: YES
set facthresha = "0.15"
# LOCKED: YES
set facthreshb = "0.19"
# LOCKED: YES
# ISWRONG: YES
set SYN_facthresha = "0.13"
# LOCKED: YES
# ISWRONG: YES
set quadpreda = "7"
# LOCKED: YES
# ISWRONG: YES
set quadpredb = "7"
# LOCKED: YES
# ISWRONG: YES
set SYN_quadpreda = "7"
# LOCKED: YES
# ISWRONG: YES
set SYN_quadpredb = "7"
# LOCKED: YES
set ML_doit = "n"
set ML_use_for_merging = "n"
# ISWRONG: YES
set ML_oversizexy = "300,300"
# ISWRONG: YES
set ML_realcellxy_outer = "200,200"
# ISWRONG: YES
set ML_realcellxy_inner = "190,190"
# ISWRONG: YES
set ML_mask_radius = "100"
set ML_threshold_method = "1"
# ISWRONG: YES
set ML_absolute_threshold = "700.0"
# ISWRONG: YES
set ML_relative_threshold = "90.0"
set ML_ref_ind = "1"
set ML_lp_method = "0"
set ML_lp_radius = "0.0"
set ML_DS_ratio = "2"
set ML_do_whiten = "y"
set ML_correct_CTF = "y"
# LOCKED: YES
set ML_rotational_symmetry = "3"
set ML_MinMaxStep_angle = "0.0,0.0,1.0"
set ML_iteration = "15"
set ML_terminate_ML = "0.02"
# ISWRONG: YES
set ML_B_factor = "-200.0"
# ISWRONG: YES
set ML_A_factor = "0.5"
set RESMIN = "200"
set RESMAX = "3.3"
set zstarrange_real = "8"
set spotlist_RESMAX = "7.0"
# ISWRONG: YES
set CS = "2.7"
set KV = "300"
set radlim = "35.0,35.0,0.0"
set domask = "n"
set createmaskinfo = "y"
set addspots = "1"
set keepOld = "n"
set mode = "0"
set ncyc = "10"
set reference = "(none)"
set overwrite = "n"
set tempkeep = "n"
set phaori = "-93.266,-56.799"
# ISWRONG: YES
set phaori_movieA = "0.0,0.0"
# ISWRONG: YES
set phaori_movieB = "0.0,0.0"
set phaoriFouFilter = "-93.266,-56.799"
# ISWRONG: YES
set phaori_ML = "0.0,0.0"
set phaori_change = "0.0,0.0"
set phaori_manual_target = "0"
set phaori_last_change = "0.000,0.000"
set diffmap_doit = "n"
set diffmap_source = "/Users/myname/Project/OtherConformation/final.aph"
set diffmap_weight = "1.0"
set rot90 = "n"
set rot180 = "n"
set revhk = "n"
set sgnxch = "n"
set revhnd = "n"
set revxsgn = "n"
set tiltanglelimit = "30.0"
set MergePhaseResidual = "37.39"
set initialization_reset = "n"
set initialization_executable = "n"
set initialization_corr_endian = "y"
# ISWRONG: YES
set diff_map1 = "merge2D.mtz"
# ISWRONG: YES
set diff_map1_name = "map1"
set diff_map2_dir = "~/data/2dx/poject"
# ISWRONG: YES
set diff_map2 = "~/data/2dx/poject/merge2D.mtz"
# ISWRONG: YES
set diff_map2_name = "map2"
set diffmap_det_significance = "y"
set diffmap_sig_algorithm = "Mixed Merge"
set diff_map_confidence = "90.0"
set diffmap_colormap = "bwr"
set diffmap_two_by_two = "n"
set diffmap_cntrs_mode = "SIG"
set diffmap_cntrs_min = "-3.0"
set diffmap_cntrs_max = "3.0"
set diffmap_cntrs_step = "0.5"
set diffmap_cntrs_below = "0"
set diffmap_fixed_plotrange = "n"
set diffmap_plotrange = "1.0"
set diffmap_plot_clean = "n"
set diffmap_threshold_method = "max"
set diffmap_plot_scalebar = "n"
set diffmap_threshold_global = "n"
set diffmap_var_factor = "1.0"
set addPhaOri = "0.0,0.0"
set addPhaOriFouFilter = "0.0,0.0"
set addBeamTilt = "0.0,0.0"
set cleanup_level = "radical"
set cleanup_mask = "n"
set merge_cleanup_location = "0"
set merge_cleanup_merge = "0"
set merge_cleanup_level = "4"
set merge_cleanup_mask = "n"
set process_cleanup_SCRATCH = "n"
set process_cleanup_FASTDISK = "y"
set gautomatch_number_particles = "."
set JREFL = "105824"
set JREFL_2D = ""
set Reflections_Unique = "59223"
set num_amplitudes_observed = "58815"
set num_phases_observed = "58815"
set num_reflections_fitted = "9489"
set num_reflections_FOM1 = "5424"
set num_reflections_FOM50 = "4527"
set overall_R_factor = "44.504"
set overall_phase_residual = "73.1"
set overall_weighted_R_factor = "38.325"
set overall_weighted_phase_residual = "41.3"
set overall_phase_residual_2D = ""
set overall_weighted_phase_residual_2D = ""
set PHARES_SYM = ""
set PHARES_NUM_SPOTS = ""
set PHARES_Merge = ""
set MergePhaseRes_slot1 = "30.84"
set MergePhaseRes_slot2 = "21.94"
set MergePhaseRes_slot3 = "32.48"
set MergePhaseRes_slot4 = "58.06"
set MergePhaseRes_slot5 = "63.51"
set MergePhaseRes_slot6 = "55.01"
set MergePhaseRes_slot7 = "57.75"
set MergePhaseRes_slot8 = "77.19"
set MergePhaseRes_slot9 = "82.09"
set MergePhaseRes_numb1 = "96"
set MergePhaseRes_numb2 = "60"
set MergePhaseRes_numb3 = "34"
set MergePhaseRes_numb4 = "11"
set MergePhaseRes_numb5 = "5"
set MergePhaseRes_numb6 = "3"
set MergePhaseRes_numb7 = "7"
set MergePhaseRes_numb8 = "7"
set MergePhaseRes_numb9 = "9"
set QVAL = "390.0"
set QVAL1 = "339.9"
set QVAL2 = "390.0"
set QVALS = "225.5"
set QVALMA = "."
set QVALAS = ""
set QVALMB = "."
set QVALBS = ""
set CALCULATEDMAG = "36970.434"
set PSMAX = "39"
set U1_IQ1 = "15"
set U1_IQ2 = "24"
set U1_IQ3 = "35"
set U1_IQ4 = "96"
set U1_IQ5 = "192"
set U1_IQ6 = "196"
set U1_IQ7 = "181"
set U1_IQ8 = "1183"
set U1_IQ9 = "2143"
set U2_IQ1 = "20"
set U2_IQ2 = "46"
set U2_IQ3 = "62"
set U2_IQ4 = "114"
set U2_IQ5 = "166"
set U2_IQ6 = "204"
set U2_IQ7 = "223"
set U2_IQ8 = "1245"
set U2_IQ9 = "2365"
set UMA_IQ1 = "."
set UMA_IQ2 = "."
set UMA_IQ3 = "."
set UMA_IQ4 = "."
set UMA_IQ5 = "."
set UMA_IQ6 = "."
set UMA_IQ7 = "."
set UMA_IQ8 = "."
set UMA_IQ9 = "."
set UAS_IQ1 = ""
set UAS_IQ2 = ""
set UAS_IQ3 = ""
set UAS_IQ4 = ""
set UAS_IQ5 = ""
set UAS_IQ6 = ""
set UAS_IQ7 = ""
set UAS_IQ8 = ""
set UAS_IQ9 = ""
set UMB_IQ1 = "."
set UMB_IQ2 = "."
set UMB_IQ3 = "."
set UMB_IQ4 = "."
set UMB_IQ5 = "."
set UMB_IQ6 = "."
set UMB_IQ7 = "."
set UMB_IQ8 = "."
set UMB_IQ9 = "."
set UBS_IQ1 = ""
set UBS_IQ2 = ""
set UBS_IQ3 = ""
set UBS_IQ4 = ""
set UBS_IQ5 = ""
set UBS_IQ6 = ""
set UBS_IQ7 = ""
set UBS_IQ8 = ""
set UBS_IQ9 = ""
set US_IQ1 = "18"
set US_IQ2 = "43"
set US_IQ3 = "63"
set US_IQ4 = "102"
set US_IQ5 = "168"
set US_IQ6 = "199"
set US_IQ7 = "229"
set US_IQ8 = "1115"
set US_IQ9 = "2133"
set RB_1 = "15"
set RB_2 = "12"
set RB_3 = "9"
set RB_4 = "7"
set RB_5 = "5"
set RB_6 = "3"
set RP_1 = "278"
set RP_2 = "38"
set RP_3 = "24"
set RP_4 = "11"
set RP_5 = "7"
set RP_6 = "7"
set DEFOCUS_TLTAXIS = "-3.711"
set DEFOCUS_TLTANG = "-26.361"
set DEFOCUS_TLTAXA = "66.977"
set DEFOCUS_TAXA = "64.563"
set DEFOCUS_TANGL = "26.690"
set LATTICE_TLTAXIS = "-88.45177"
set LATTICE_TLTANG = "26.69375"
set LATTICE_TLTAXA = "66.97777"
set LATTICE_TAXA = "64.56303"
set LATTICE_TANGL = "26.69375"
set TTREFINE_TLTAXIS = "--"
set TTREFINE_TLTANG = "--"
set TTREFINE_TLTAXA = "--"
set TTREFINE_TAXA = "--"
set TTREFINE_TANGL = "--"
set MERGE_TLTAXIS = "89.503"
set MERGE_TLTANG = "-26.640"
set MERGE_TLTAXA = "-25.659"
set MERGE_TAXA = "66.783"
set MERGE_TANGL = "26.640"
set DEFOCUS_ACTIVE = "2"
set FFT_done = "y"
set DEFOCUS_done = "y"
set SPOTS_done = "y"
set UNBENDING_done = "y"
set ML_done = "n"
set CTF_done = "y"
set PHASEORI_done = "y"
set MERGING_done = "n"
set REPROCESSING_done = "n"
set dummy = "1"
set SPR_IMGS_DIR = ""
set SPR_MERGEFILE = ""
set SPR_STACKS_DIR = ""
set SPR_FREALIGN_DIR = ""
set SPR_PICKING_DIR = ""
set SPR_STACK_ROOTNAME = ""
set SPR_FSC_DIR = ""
set SPR_FRC_DIR = ""
set SPR_STATS_DIR = ""
#
#=============================================================================
#