############################################################################## # The sNum section. Information belonging to the currently loaded structure ############################################################################## snum .short_caption = Current Structure .caption = Settings that are saved with each structure { current_process = "" .type = str current_process_details = "" .type = str current_process_status = "" .type = str current_process_diagnostics = "hkl" .type = str current_r1 = 0 .type = float init .short_caption = Skipps history creation and inversion analysis for internal \ routines requiring structure refinement .expert_level = 1 { skip_routine = False .type = bool .expert_level = 1 } ED .short_caption = ED parameters { combined_stats = False .type = bool } bonds { mask = 48 .type = int bzoom = 100 .type = int colour = elements .type = str colours = @@elements 5@4278223103@4278255615@@orange '5@4282071867@4286611584@@dark grey' .type = strings } atoms { style = matt.glds .type = str azoom = 100 .type = int } experimental{ } metadata{ resolved_conflict_items = "" .type = strings show_all_cif_sources = False .type = bool force_metacif = False .type = bool } ccdc{ note_to_staff = ++ Thank you! ++ .type = str submission_type = +++ Please Choose +++ .type = str } cds{ error_a = 3 .type = int error_s = 2 .type = int } current_result{ cif = None .type = path fcf = None .type = path } selection{ scope{ latest = "" .type = str model{ is_chosen = True .type = bool } disorder{ is_chosen = True .type = bool } geometry{ is_chosen = True .type = bool } symmetry{ is_chosen = True .type = bool } report{ is_chosen = True .type = bool } display{ is_chosen = True .type = bool } } } hkl{ hkl_stat_file = None .type = path completeness_full = 0 .type = float fcf = None .type = path d_min = None .type = float } smtbx .short_caption = Solution & Refinement { inelastic_form_factor_table = henke sasaki *brennan .type = choice atomic_form_factor_table = *it1992 wk1995 n_gaussian electron neutron .type = choice electron_table_name = *None Custom 'Peng-1996' 'Peng-1999' 'UCLA-2022' 'CAP-2022' .type = choice secondary_ch2_angle = idealise refine *shelxl .type = choice sump = *constraint restraint .type = choice } solution .short_caption = Structure Solution { vss = 0 .type = float vata = 0 .type = float program = ShelXS ShelXS-1997 ShelXS-1986 XS XT ShelXT '*olex2.solve' XM ShelXD ShelXD-1997 SIR2002 SIR2004 SIR2008 SIR2011 Superflip Unknown ShelXS-2013 ShelXS86 ShelXD-2013 .type = choice method = 'Dual Space' '*Charge Flipping' 'Direct Methods' 'Patterson Method' 'Structure Expansion' 'Intrinsic Phasing' Unknown .type = choice graphical_output = False .type = bool current_atomic_volume = None .type = float Sir2002{ gui = True .type = bool } Sir2004{ gui = False .type = bool } Sir2008{ gui = False .type = bool } ShelXS .short_caption = 'Program specific command line' { command_line = '' .type = str } ShelXD .short_caption = 'Program specific command line' { command_line = '' .type = str } ShelXT .short_caption = 'Program specific command line' { command_line = '' .type = str } XS .short_caption = 'Program specific command line' { command_line = '' .type = str } XM .short_caption = 'Program specific command line' { command_line = '' .type = str } XT .short_caption = 'Program specific command line' { command_line = '' .type = str } } htab{ distance = 2.9 .type = float angle = 140 .type = float } refinement .short_caption = Structure Refinement { ata = 0 .type = float data_parameter_ratio = None .type = float parameters = None .type = int data = None .type = int coverge_max_shift = 0.001 .type = float max_shift_over_esd = None .type = float max_shift_over_esd_atom = None .type = str max_shift_site = None .type = float max_shift_site_atom = None .type = str max_shift_u = None .type = float max_shift_u_atom = None .type = str max_peak = None .type = float max_hole = None .type = float res_rms = None .type = float goof = None .type = float flack_str = None .type = str hooft_str = None .type = str parson_str = None .type = str expected_peaks = None .type = int has_h = False .type = bool is_anis = False .type = bool is_fully_assigned = False .type = bool last_R1 = n/a .type = str .expert_level = 2 last_wR2 = n/a .type = str .expert_level = 2 graphical_output = False .type = bool program = XL XH ShelXH-1997 ShelXL ShelXL-1997 '*olex2.refine'\ Unknown .type = choice method = 'Least Squares' CGLS '*Gauss-Newton' 'Levenberg-Marquardt' \ 'Full Matrix' Unknown .type = choice sg_list = None .type = str .expert_level = 1 max_cycles = 4 .type = int(value_min=0) .help = The maximum number of refinement cycles to be performed max_peaks = 20 .type = int .help = The maximum number of electron density peaks to be returned \ after refinement manual_q_peak_override = 0 .type = int .help = Retain manually set numbers of peaks update_weight = True .type = bool .help = Automatically update the weight instruction before the next \ refinement update_weight_maxR1 = 15 .type = float .help = The maximum R1 value below which weighting scheme will be updated automatically suggested_weight = None .type = floats(size=2) .help = The weighting scheme parameters suggested by the refinement \ program in a previous cycle refine_extinction = 1 .type = int refine_extinction_tickbox = False .type = bool refine_swat = 1 .type = int refine_swat_tickbox = False .type = bool original_formula = None .type = str .expert_level = 1 use_solvent_mask = False .type = bool recompute_mask_before_refinement = False .type = bool recompute_mask_before_refinement_prg = *Olex2 Platon .type = choice auto_add_masked_moieties = True .type = bool check_absolute_structure_after_refinement = True .type = bool cifmerge_after_refinement = True .type = bool check_PDF = True .type = bool ShelXL .short_caption = 'Program specific command line' { command_line = '' .type = str } ShelXL97 .short_caption = 'Program specific command line' { command_line = '' .type = str } XLMP .short_caption = 'Program specific command line' { command_line = '' .type = str } auto .short_caption = Autotidy { max_peaks = False .type = bool set_q_peaks = True .type = bool assignQ = 2.0 .type = float(value_min=0.0) .help = Assign all residual electron density peaks greater than the \ given cutoff value as a Carbon atom pruneU = 0.1 .type = float(value_min=0.0) .help = Delete all atoms where the Ueq is greater than the given cutoff pruneQ = 1.5 .type = float(value_min=0.0) .help = Delete all residual electron density peaks smaller than \ the given cutoff value promote = 0.1 .type = float assemble = False .type = bool .help = Move all atoms or fragments of the asymmetric unit as \ close together as possible tidy = False .type = bool .help = Automatically tidy the structure after refinement according \ to the settings invert = True .type = bool .help = If set to TRUE, the structure will be automatically inverted if the inversion seems necessary remove_anharm = False .type = bool .help = If set to TRUE, the structure will be automatically harmonized in case of bad PDF } } twinning{ olex2{ do_long = False .type = bool number_laws = 1 .type = int overlap_threshold=0.004 .type = float max_index = 5 .type = int rotation_fraction = 12 .type = int threshold = 0.002 .type = float threshold_sphere= 0.002 .type=float size_sphere=10 .type=int } } display_quality = 2 .type = int(value_min=1, value_max=3) image .short_caption = Structure Images { if_file_exists = *ask increment replace .type = choice name = None .type = str trim_border_colour = #dedede .type = str bitmap .short_caption = png, jpg, bmp ... { name = None .type = str type = *png jpg bmp tif png/s .type = choice atom_label{ font_name = #olex2.fnt:frb_18 .type = str font_colour = "2049;0" .type = str } bond_label{ font_name = #olex2.fnt:frb_14 .type = str } } povray { name = None .type = str type = *pov .type = choice } ps .short_caption = ORTEP - Postscript { name = None .type = str type = *eps .type = choice colour_line= " " .type = str colour_bond= " " .type = str colour_fill= " " .type = str perspective = " " .type = str outline_width = 1.0 .type = float octant_width = 1.0 .type = float pie_width = 0.6 .type = float octant_count = 5 .type = int octant_atoms = -C .type = str h_bond_width = 0.6 .type = float bond_width = 0.7 .type = float font_weight = 1.2 .type = float atom_label{ font_name = @ .type = str font_size = 15 .type = int font_colour = #00000 .type = colour font_weight = 1.0 .type = float } bond_label{ font_name = @ .type = str font_size = 8 .type = int font_colour = #00000 .type = colour font_weight = 1.0 .type = float } } image_series .short_caption = Movie { rotation_around_axis=2 .type = int degrees_of_rotation=1.0 .type = float number_of_frames=30 .type=int size_of_frames=0.2 .type=float } } display .short_caption = Display styles for the molecule { collections = "" .type = str } shelx_output = True .type = bool history { current_node = None .type = str .expert_level = 2 condensed_tree = True .type = bool } autochem_current_solution = "Autochem 01" .type = str auto_hydrogen_naming = True .type = bool dimas .expert_level=2 { progress_status = None .type = str progress_comment = None .type = str reference_ccdc_number = None .type = str reference_csd_refcode = None .type = str reference_publ_authors = None .type = str reference_journal_name = None .type = str reference_journal_volume = None .type = str reference_journal_pages = None .type = int(value_min=1) reference_journal_year = None .type = int(value_min=1800, value_max=2100) reference_comment = None .type = str } metacif .short_caption = Metadata for CIF { publ_author_names = None .type = str abs_file = None .type = path .expert_level = 1 sad_file = None .type = path .expert_level = 1 pcf_file = None .type = path .expert_level = 1 p4p_file = None .type = path .expert_level = 1 smart_file = None .type = path .expert_level = 1 saint_file = None .type = path .expert_level = 1 frames_file = None .type = path .expert_level = 1 integ_file = None .type = path .expert_level = 1 cad4_file = None .type = path .expert_level = 1 crystal_clear_file = None .type = path .expert_level = 1 twin_file = None .type = path .expert_level = 1 result_fcf_file = None .type = path .expert_level = 1 result_cif_file = None .type = path .expert_level = 1 abs_type = twinabs sadabs .type = choice list_sad_files = None .type = strings .expert_level = 2 list_abs_files = None .type = strings .expert_level = 2 list_pcf_files = None .type = strings .expert_level = 2 list_p4p_files = None .type = strings .expert_level = 2 list_smart_files = None .type = strings .expert_level = 2 list_saint_files = None .type = strings .expert_level = 2 list_frames_files = None .type = strings .expert_level = 2 list_integ_files = None .type = strings .expert_level = 2 list_cad4_files = None .type = strings .expert_level = 2 list_crystal_clear_files = None .type = strings .expert_level = 2 list_result_cif_files = None .type = strings .expert_level = 2 list_result_fcf_files = None .type = strings .expert_level = 2 user_input_variables = None .type = str .expert_level = 2 list_twin_files = None .type = strings .expert_level = 2 user_modified = None .type = strings .expert_level = 2 user_added = None .type = strings .expert_level = 2 user_removed = None .type = strings .expert_level = 2 } report .short_caption = Report Metadata { publication_style = general .type = str publication_paper = "" .type = str merge_these_cifs = "" .type = strings type = "Structure Report" .type = str date_format = "%d-%m-%Y" .type = str date_submitted = None .type = str date_collected = None .type = str date_completed = None .type = str total_time = 0 .type = int frame_images = None .type = strings notes_file = None .type = path crystal_images_path = None .type = str crystal_mounting_method = None .type = str crystal_mounting_notes = "Nothing special was noted when selecting and mounting the crystal" .type = str submission_special_instructions = "No special instructions were received" .type = str submission_original_sample_id = None .type = str data_collection_notes = "" .type = str operator = None .type = str submitter = None .type = str diffractometer = None .type = str diffractometer_image = "" .type = str title = FileName() .type = path image = "No Image" .type = str image_border = 2 .type = int structure{ smiles_string = "" .type = str } lab{ logo = "" .type = str name = "" .type = str } tex{ page = 'a4paper' .type = str fontsize = '10pt' .type = str fleqn = 'fleqn' .type = str table1_caption = 'Crystal data and structure refinement for' .type = str } } eden_fine_value = 0 .type = int eden_coarse_value = 1 .type = int eden_value = None .type = float xgrid { view = *wire 2D plane surface points contour 'contour+plane' .type = choice extended = False .type = bool value = 0.0 .type = float heat_colours = 2 3 *5 7 .type = choice contours = 15 .type = int step = 0 .type = float fix = 0 .type = float slider_scale = 10 .type = int depth = 0 .type = float size = 15 .type = int scale = 0.1 .type = float } map { source = *olex fcf cctbx .type = choice type = *diff fcalc tomc fobs fcfmc PDF mask .type = choice PDF_second_order = True .type = bool PDF_third_order = True .type = bool PDF_fourth_order = True .type = bool mask = True .type = bool mask_d = 1.0 .type = float scale = *external external-forced sigma shelx .type = choice resolution = 0.1 .type = float } calcvoid { resolution = 0.2 .type = float precise = True .type = bool distance = 0.0 .type = float } calcsolv { probe = 1.2 .type = float grid = 0.2 .type = float } masks { original_hklsrc = None .type = path type = *mask f_mask f_model .type = choice solvent_radius = 1.2 .type = float shrink_truncation_radius = 1.2 .type = float resolution_factor = 1/4 .type = float use_set_completion = True .type = bool update_cif = False .type = bool special_detail_button_text = 'Use & Edit' .type = str special_detail_colour = #ff0000 .type = colour } cif { htab_max_d = 2.9 .type = float htab_min_angle = 120 .type = float report_rtabs = True .type = bool report_vars = True .type = bool dataname = '' .type = str } olex_conres = RRINGS .type = str refinement_banner_slide = 82 .type = int } olex2 .short_caption = Olex2 Internal Settings { news_img_src = http://www.olex2.org/adverts/olex2adverts.txt .type = str splash_img_src = http://www.olex2.org/adverts/splash.txt .type = str stop_current_process = False .type = bool is_online = True .type = bool is_logged_on = False .type = bool mac_address = "" .type = str verbose = False .type = bool last_version = 12 .type = int in_mode = None .type = str full_mode = None .type = str short_mode = None .type = str debug = False .type = bool dev_mode = False .type = bool force_images = False .type = bool sNum_id_string = None .type = str main_toolbar_vline_position = 100 .type = int hover_buttons = True .type = bool news_img_link_url = "www.olex2.org" .type = str pdfplugin{ path = 'BaseDir()/pdf-plugin/qt4-pdf.exe' .type = str } network = True .type = bool auto_gen_disp = True .type = bool samples{ url = https://secure.opencryst.org/samples .type = str .help = Location of online sample structures. } ccdc{ url = http://ccdc.opencryst.org/deposit http://ccdc1.opencryst.org/deposit .type = strings .help = List of the OlexSys servers used to forward requests to the CCDC pop{ name=ccdc .type = str htm = \etc\gui\blocks\templates\pop_ccdc_submit.htm .type = str width = 610 .type = int height = automatic .type = str auto_height_constant = 280 .type = int auto_height_line = 20 .type = int position = center .type = str border = 10 .type = int } } refinement { stop_ED_ASAP = True .type = bool } } programs .short_caption = Program Settings { solution .short_caption = Structure Solution { smtbx .short_caption = olex2.solve { cf .short_caption = Charge Flipping { amplitude_type = F E *quasi-E .type = choice max_attempts_to_get_phase_transition = 5 .type = int max_attempts_to_get_sharp_correlation_map = 5 .type = int max_solving_iterations = 500 .type = int } } Sir2002 .short_caption = olex2.solve { gui = False .type = bool } Sir2004 .short_caption = olex2.solve { gui = False .type = bool } Sir2008 .short_caption = olex2.solve { gui = False .type = bool } } } user .short_caption = User Specific { sample_dir = "" .type = str customisation_dir = "" .type = str cif_templates_dir = "" .type = str email = "" .type = str reference = "" .type = str def_style_scene_src_dir = BaseDir()/etc/styles/ .type = str def_style = 'default' .type = str def_scene = 'default' .type = str brad = 10 .type = int solo = True .type = bool .help = "Only one top-level tool can be open at any one time" solo_exceptions = start .type = strings auto_close_settings_panel = False .type = bool auto_insert_user_ins = "MORE -1, CONF, BOND \$H" .type = str folder_view_root = None .type = path use_fader = 0 .type = float show_tooltips = 1 .type = int show_info = 0 .type = int show_legend = True .type = bool auto_save_view = False .type = bool expert_level = 0 .type = int alert_delete_history = Y .type = str .expert_level = 1 alert_overwrite_history = Y .type = str .expert_level = 1 alert_uninstall_plugin = Y .type = str .expert_level = 1 alert_solve_anyway = Y .type = str .expert_level = 1 start_where = home .type = str remember_last = True .type = bool report_style = styles/default.css .type = str report_template = templates/default.htm .type = str report_footer = templates/footer.htm .type = str report_journal_style = rsc .type = str report_label_style = 0 .type = int legend{ horizontal = *l r .type = choice vertical = *t b .type = choice padding = 60 .type = str } edit_ins_atom_order = ins_atom .type = str parts{ keep_unique = True .type = bool select = True .type = bool } solution{ run_auto_vss = False .type = bool default_program = "" .type = str default_method = "" .type = str } refinement{ default_program = "" .type = str default_method = "" .type = str hide_nsff = False .type = bool .expert_level = 2 refln_loop = False .type = bool use_openmp = False .type = bool has_HT = True .type = bool openmp_mem = 2000 .type = int thread_n = -1 .type = str diagnostics = False .type = bool client_mode = False .type = bool shelxl_convergence = 0.000 .type = float shelxl_convergence_use = True .type = bool } masks{ based_on = *ASU FU Cell .type = choice v_over_e{ upper = 8 .type=float lower = 2 .type = float } } graphs .short_caption = Analysis Graphs { non_highlight_colour = "#ababab" .type = str non_highlight_width_factor = 2 .type = float highlight_colour = "auto" .type = str matplotlib{ style = *seaborn-whitegrid fivethirtyeight .type = choice colour_map = "tab20c" .type = str legend_in_out = * outside best .type = choice legend_vertical = *upper center lower .type = choice legend_horizontal = left center *right .type = choice legend_manual_position = 1 0.8 .type = str print_byline = True .type = bool grid = False .type = bool ax_colour = #666666 .type = str fig_width = 8 .type = int fig_height = 8 .type = int font_name = 'Consolas' .type = str title_fontsize = 20 .type=int subtitle_fontsize = 14 .type=int subplot_top_gap = 0.95 .type=float tick_fontsize = 14 .type=int axis_fontsize = 14 .type=int highlight_colour = #FFAC1C .type = str subplot_ratio = 3 .type = int stack = False .type = bool ax1{ colour = auto_scale .type = str style = 'line' .type = str marker = "." .type = str marker_size = 1 .type = int marker_face_colour = #ffffff .type = str marker_edge_colour = #888888 .type = str marker_edge_width = 1 .type = int line_width = 1 .type = int linestyle = solid .type = str } ax2{ colour = auto_scale .type = str style = 'line' .type = str marker = "." .type = str marker_size = 1 .type = int marker_face_colour = #ff88ff .type = str marker_edge_colour = #ff0000 .type = str marker_edge_width = 1 .type = int line_width = 1 .type = int linestyle = solid .type = str } } program_analysis { font_scale = 0.03 .type = float(value_min=0.0) size_x = None .type = int(value_min=0) size_y = None .type = int(value_min=0) max_bars = 12 .type = int all_in_one_history = False .type = bool y_scale_factor = 3 .type = int } reflections { n_divisions = 5 .type = int(value_min=0) size_x = 900 .type = int(value_min=0) size_y = 500 .type = int(value_min=0) font_scale = 0.02 .type = float(value_min=0.0) marker_1 { fill = (255,150,50) .type = colour border = (127,75,25) .type = colour size_factor = 1./80 .type = float } marker_2 { fill = (160,182,206) .type = colour border = (80,91,103) .type = colour size_factor = 1./120 .type = float } marker_3 { fill = (140,182,206) .type = colour border = (80,91,103) .type = colour size_factor = 1./120 .type = float } marker_4 { fill = (120,182,206) .type = colour border = (80,91,103) .type = colour size_factor = 1./120 .type = float } marker_5 { fill = (100,182,206) .type = colour border = (80,91,103) .type = colour size_factor = 1./80 .type = float } function_1 { colour = (0,0,0) .type = colour } function_2 { colour = (0,0,255) .type = colour } function_3 { colour = (255,0,0) .type = colour } function_4 { colour = (0,255,0) .type = colour } function_5 { colour = (0,255,255) .type = colour } function_6 { colour = (255,255,0) .type = colour } function_7 { colour = (255,0,255) .type = colour } function_8 { colour = (128,128,128) .type = colour } cumulative_intensity .short_caption = "Cumulative Intensity" .caption = "Cumulative Intensity Distribution" .help = "Cumulative-Intensity-Distribution" { n_bins = 20 .type = int(value_min=1) .help = Number of bins .caption = %Bins% output_csv_file = False .type = bool .caption = "%Output% csv" } wilson_plot .short_caption = "Wilson Plot" .caption = "Wilson Plot" .help = "Wilson-Plot" { n_bins = 10 .type = int(value_min=1) .help = Number of bins .caption = %Bins% method = *Olex2 cctbx .type = choice .caption = "%Method%" output_csv_file = False .type = bool .caption = "%Output% csv" } systematic_absences .short_caption = "Systematic Absences" .caption = "Systematic Absences" .help = "Systematic-Absences" { output_csv_file = False .type = bool .caption = "%Output% csv" } fobs_fcalc .short_caption = "Fobs-Fcalc" .caption = "Fobs-Fcalc" .help = "Fobs-vs-Fcalc" { output_csv_file = False .type = bool .caption = "%Output% csv" } iobs_icalc .short_caption = "Iobs-Icalc" .caption = "Iobs-Icalc" .help = "Iobs-vs-Icalc" { output_csv_file = False .type = bool .caption = "%Output% csv" } fobs_over_fcalc .short_caption = "Fobs/Fcalc" .caption = "Fobs/Fcalc vs resolution" .help = "Fobs/Fcalc-vs-resolution" { resolution_as = two_theta *d_spacing d_star_sq stol stol_sq .type = choice .caption = "Resolution as" binning = True .type=bool .caption= "Binning" n_bins = 10 .type = int(value_min=1) .help = Number of bins .caption = %Bins% output_csv_file = False .type = bool .caption = "%Output% csv" } scale_factor_vs_resolution .short_caption = "scale vs res." .caption = "Scale factor vs resolution" .help = "Scale-factor-vs-resolution" { resolution_as = two_theta *d_spacing d_star_sq stol stol_sq .type = choice .caption = "Resolution as" n_bins = 10 .type = int(value_min=1) .help = Number of bins .caption = %Bins% output_csv_file = False .type = bool .caption = "%Output% csv" } r1_factor_vs_resolution .short_caption = "R1 vs res." .caption = "R1 vs. Resolution" .help = "R1-factor-vs-resolution" { title = "R1 vs. Resolution" .type = str resolution_as = *two_theta d_spacing d_star_sq stol stol_sq .type = choice .caption = "Resolution as" n_bins = 10 .type = int(value_min=1) .help = Number of bins .caption = %Bins% output_csv_file = False .type = bool .caption = "%Output% csv" } i_over_sigma_vs_resolution .short_caption = "I/sig vs res." .caption = "I/sigma vs Resolution" .help = "R1-factor-vs-resolution" { title = "I/sigma(I) vs. Resolution" .type = str resolution_as = *two_theta d_spacing d_star_sq stol stol_sq .type = choice .caption = "Resolution as" n_bins = 20 .type = int(value_min=1) .help = Number of bins .caption = %Bins% output_csv_file = False .type = bool .caption = "%Output% csv" } cc_half_vs_resolution .short_caption = "cc_half_vs_resolution" .caption = "cc_half_vs_resolution" .help = "cc_half_vs_resolution" { title = "cc_half_vs_resolution" .type = str resolution_as = *two_theta d_spacing d_star_sq stol stol_sq .type = choice .caption = "Resolution as" n_bins = 20 .type = int(value_min=1) .help = Number of bins .caption = %Bins% output_csv_file = False .type = bool .caption = "%Output% csv" } rmerge_vs_resolution .short_caption = "Rmerge vs resolution" .caption = "Rmerge vs resolution" .help = "Rmerge vs resolution" { title = "Rmerge vs resolution" .type = str resolution_as = *two_theta d_spacing d_star_sq stol stol_sq .type = choice .caption = "Resolution as" n_bins = 20 .type = int(value_min=1) .help = Number of bins .caption = %Bins% output_csv_file = False .type = bool .caption = "%Output% csv" } completeness .short_caption = "Completeness Plot" .caption = "Completeness Plot" .help = "Completeness-Plot" { reflections_per_bin=20 .type = int(value_min=1) .caption = "Reflections per bin" resolution_as = two_theta *d_spacing d_star_sq stol stol_sq .type = choice .caption = "Resolution as" output_csv_file = False .type = bool .caption = "%Output% csv" } normal_probability .short_caption = "Normal Probability Plot" .caption = "Normal Probability Plot" .help = "Normal-Probability-Plot" { output_csv_file = False .type = bool .caption = "%Output% csv" } bijvoet_differences_probability_plot .short_caption = "Bijvoet Differences Probability Plot" .caption = "Bijvoet Differences Probability Plot" .help = "Bijvoet-differences-NPP" { output_csv_file = False .type = bool .caption = "%Output% csv" use_students_t = False .type = bool .caption = "%Student's t%" source = *Olex2 fcf .type = choice .caption = "%Source%" } bijvoet_differences_scatter_plot .short_caption = "Bijvoet Differences Scatter Plot" .caption = "Bijvoet Differences Scatter Plot" .help = "Bijvoet-differences-scatter-plot" { output_csv_file = False .type = bool .caption = "%Output% csv" use_students_t = False .type = bool .caption = "%Student's t%" } } } diagnostics { debug = False .type = bool scale = 2 .type = int scopes = hkl refinement .type = strings refinement{ dpr{ halve_for_non_centro = False .type = bool display = "Data/Parameter" .type = str op = "smaller" .type = str value_format= "1f" .type = str grade1 = 4 .type = float grade2 = 6 .type = float grade3 = 8 .type = float grade4 = 10 .type = float href = Data/Parameter .type = str target = "Data/Parameter Ratio" .type = str } hooft_str{ display = "Hooft" .type = str href = "spy.make_reflection_graph(wilson_plot)>>spy.make_reflection_graph(cumulative_intensity)" .type = str target = "Hooft Parameter. - This should be close to 0 - The e.s.d. value must be small - 'inv -f' to invert" .type = str } flack_esd{ display = "FE" .type = str op = "smaller" .type = str value_format= "3f" .type = str grade1 = 0.04 .type = float grade2 = 0.05 .type = float grade3 = 0.06 .type = float grade4 = 0.07 .type = float href = Flack e.s.d .type = str target = "Flack Parameter esd" .type = str } flack_val{ display = "FV" .type = str op = "smaller" .type = str value_format= "3f" .type = str grade1 = 0.02 .type = float grade2 = 0.04 .type = float grade3 = 0.08 .type = float grade4 = 0.10 .type = float href = Flack Value .type = str target = "Flack Parameter Value" .type = str } R1{ op = "smaller" .type = str value_format= "3f" .type = str grade1 = 0.05 .type = float grade2 = 0.10 .type = float grade3 = 0.15 .type = float grade4 = 0.20 .type = float top = 0.30 .type = float display = "R1" .type = str } wR2{ op = "smaller" .type = str value_format= "3f" .type = str grade1 = 0.10 .type = float grade2 = 0.20 .type = float grade3 = 0.30 .type = float grade4 = 0.40 .type = float top = 0.50 .type = float display = "wR2" .type = str } max_shift_site{ op = "smaller" .type = str value_format= "3f" .type = str grade1 = 0.001 .type = float grade2 = 0.005 .type = float grade3 = 0.010 .type = float grade4 = 0.015 .type = float top = 0.15 .type = float display = "Max Shift" .type = str href = atom .type = str target = "Select the site with the largest shift. NOTE: The shift may be caused by EXTI!" .type = str } max_shift_over_esd { op = "smaller" .type = str value_format= "3f" .type = str grade1 = 0.001 .type = float grade2 = 0.005 .type = float grade3 = 0.010 .type = float grade4 = 0.015 .type = float top = 0.15 .type = float display = "Shift" .type = str href = atom .type = str target = "Select the site with the largest shift. NOTE: The shift may be caused by EXTI!" .type = str } _refine_ls_shift_over_su_max { op = "smaller" .type = str value_format= "3f" .type = str grade1 = 0.001 .type = float grade2 = 0.005 .type = float grade3 = 0.010 .type = float grade4 = 0.015 .type = float top = 0.15 .type = float display = "Shift/esd" .type = str href = None .type = str target = "Select the atom with the largest shift" .type = str } max_shift_u{ op = "smaller" .type = str value_format= "3f" .type = str grade1 = 0.001 .type = float grade2 = 0.005 .type = float grade3 = 0.010 .type = float grade4 = 0.015 .type = float top = 0.15 .type = float display = "Max dU" .type = str href = atom .type = str target = "Select the atom with the largest U shift" .type = str } max_peak{ op = "smaller" .type = str display = "Max Peak" .type = str value_format= "1f" .type = str grade1 = 0.51 .type = float grade2 = 1.01 .type = float grade3 = 2.01 .type = float grade4 = 3.01 .type = float top = 5 .type = float href = sel Q1 .type = str target = "Select the largest peak" .type = str } _refine_diff_density_max{ op = "smaller" .type = str display = "Max Peak" .type = str value_format= "1f" .type = str grade1 = 0.51 .type = float grade2 = 1.01 .type = float grade3 = 2.01 .type = float grade4 = 3.01 .type = float top = 5 .type = float href = None .type = str } max_hole{ op = "greater" .type = str display = "Min Peak" .type = str value_format= "1f" .type = str grade1 = -0.51 .type = float grade2 = -1.01 .type = float grade3 = -2.01 .type = float grade4 = -3.01 .type = float top = -5 .type = float href = echo "Please add PLAN -n to your ins file first" .type = str } _refine_diff_density_min{ op = "greater" .type = str display = "Min Peak" .type = str value_format= "1f" .type = str grade1 = -0.51 .type = float grade2 = -1.01 .type = float grade3 = -2.01 .type = float grade4 = -3.01 .type = float top = -5 .type = float href = None .type = str } goof{ op = "between" .type = str value_format= "3f" .type = str display = "GooF" .type = str soll = 1.0 .type = float grade1 = 0.1 .type = float grade2 = 0.2 .type = float grade3 = 0.3 .type = float grade4 = 0.5 .type = float top = 0.5 .type = float href = "spy.gui.UpdateWeight()>>html.Update" .type = str target = "Update the weighting scheme" .type = str } expected_peaks{ op = "smaller" .type = str display = "Missing" .type = str value_format= "0f" .type = str grade1 = 0 .type = int grade2 = 1 .type = int grade3 = 2 .type = int grade4 = 5 .type = int top = 10 .type = int href = echo Fred .type = str } } hkl{ MaxD{ value_format= "2f" .type = str display = "d max" .type = str } MinD{ value_format= "2f" .type = str display = "d min" .type = str op = "smaller" .type = str grade1 = 0.75 .type = float grade2 = 0.841 .type = float grade3 = 0.86 .type = float grade4 = 0.88 .type = float top = 1.0 .type = float } MeanIOverSigma{ op = "greater" .type = str display = "Mean I/σ" .type = str value_format= "1f" .type = str grade1 = 15 .type = float grade2 = 12 .type = float grade3 = 9 .type = float grade4 = 6 .type = float top = 25 .type = float href = "spy.make_reflection_graph(i_over_sigma_vs_resolution)" .type = str target = "Mean signal to noise ratio. Click to see the graph" .type = str } Rint{ op = "smaller" .type = str display = "Rint" .type = str value_format= "2%" .type = str grade1 = 0.04 .type = float grade2 = 0.06 .type = float grade3 = 0.10 .type = float grade4 = 0.15 .type = float top = 0.15 .type = float href = "spy.make_reflection_graph(rmerge_vs_resolution)" .type = str target = "Internal R factors. Click to see the graph" .type = str } Completeness{ op = "greater" .type = str display = "Compl." .type = str value_format= "0%" .type = str grade1 = 0.99 .type = float grade2 = 0.95 .type = float grade3 = 0.90 .type = float grade4 = 0.80 .type = float top = 0.15 .type = float href = "spy.make_reflection_graph(completeness)>>hklstat" .type = str resolution = max *full .type = choice target = "Show reflection statistics - hkl file must be present" .type = str } } } diagnostics_ed { refinement{ dpr{ grade1 = 4 .type = float grade2 = 6 .type = float grade3 = 8 .type = float grade4 = 10 .type = float } flack_esd{ grade1 = 0.04 .type = float grade2 = 0.05 .type = float grade3 = 0.06 .type = float grade4 = 0.07 .type = float } flack_val{ grade1 = 0.02 .type = float grade2 = 0.04 .type = float grade3 = 0.08 .type = float grade4 = 0.10 .type = float } R1{ grade1 = 0.10 .type = float grade2 = 0.15 .type = float grade3 = 0.20 .type = float grade4 = 0.25 .type = float top = 0.40 .type = float } wR2{ grade1 = 0.10 .type = float grade2 = 0.20 .type = float grade3 = 0.30 .type = float grade4 = 0.40 .type = float top = 0.50 .type = float } max_shift_site{ grade1 = 0.001 .type = float grade2 = 0.005 .type = float grade3 = 0.010 .type = float grade4 = 0.015 .type = float top = 0.15 .type = float } max_shift_over_esd { grade1 = 0.001 .type = float grade2 = 0.005 .type = float grade3 = 0.010 .type = float grade4 = 0.015 .type = float top = 0.15 .type = float } _refine_ls_shift_over_su_max { grade1 = 0.001 .type = float grade2 = 0.005 .type = float grade3 = 0.010 .type = float grade4 = 0.015 .type = float top = 0.15 .type = float } max_shift_u{ grade1 = 0.001 .type = float grade2 = 0.005 .type = float grade3 = 0.010 .type = float grade4 = 0.015 .type = float top = 0.15 .type = float } max_peak{ grade1 = 0.51 .type = float grade2 = 1.01 .type = float grade3 = 2.01 .type = float grade4 = 3.01 .type = float top = 5 .type = float } _refine_diff_density_max{ grade1 = 0.51 .type = float grade2 = 1.01 .type = float grade3 = 2.01 .type = float grade4 = 3.01 .type = float top = 5 .type = float } max_hole{ grade1 = -0.51 .type = float grade2 = -1.01 .type = float grade3 = -2.01 .type = float grade4 = -3.01 .type = float top = -5 .type = float } _refine_diff_density_min{ grade1 = -0.51 .type = float grade2 = -1.01 .type = float grade3 = -2.01 .type = float grade4 = -3.01 .type = float top = -5 .type = float } goof{ soll = 1.0 .type = float grade1 = 0.1 .type = float grade2 = 0.2 .type = float grade3 = 0.3 .type = float grade4 = 0.5 .type = float top = 0.5 .type = float } } hkl{ MinD{ grade1 = 0.75 .type = float grade2 = 0.841 .type = float grade3 = 0.86 .type = float grade4 = 0.88 .type = float } MeanIOverSigma{ grade1 = 4 .type = float grade2 = 3 .type = float grade3 = 2 .type = float grade4 = 1 .type = float } Rint{ grade1 = 0.10 .type = float grade2 = 0.15 .type = float grade3 = 0.20 .type = float grade4 = 0.25 .type = float } Completeness{ grade1 = 0.95 .type = float grade2 = 0.90 .type = float grade3 = 0.85 .type = float grade4 = 0.80 .type = float } } } diagnostics{ pin_scopes = True .type = bool use_matplotlib = False .type = bool use_plotly = False .type = bool plotly_username = "" .type = str plotly_password = "" .type = str save_file= False .type = bool } report{ db_location = DataDir()/db .type = str db_name = olex2.sqlite .type = str styles_base_path = "BaseDir()/etc/CIF/styles" .type = str templates_base_path = "BaseDir()/etc/CIF/templates" .type = str template = default.htm .type = str style = default.css .type = str template_full_path = templates/default.htm .type = path footer_full_path = templates/footer.htm .type = path style_full_path = styles/default.css .type = path footer = templates/footer.htm .type = str journal_style = rsc .type = str lab{ logo = "BaseDir()/etc/site/logo.png" .type = str name = OlexSys Crystallographic Services .type = str } diffractometer_image = "BaseDir()/util/pyUtil/PluginLib/plugin-AutoChem2/images/gemini.jpg" .type = str } bonds { mask = 48 .type = int bzoom = 100 .type = int colour = elements .type = str colours = @@elements 5@4278223103@4278255615@@orange '5@4282071867@4286611584@@dark grey' .type = strings } atoms { style = matt.glds .type = str azoom = 100 .type = int } auto_refine_after_anis = True .type = bool auto_compact = True .type = bool cif{ autorefine_if_no_cif_for_cifmerge = True .type = bool finalise = *Ignore Include Exclude .type = choice checkcif{ url = https://checkcif.iucr.org/cgi-bin/checkcif_hkl.pl .type = str .help = The URL to which the cif file will be sent hkl_url = https://checkcif.iucr.org/cgi-bin/checkcif_hkl.pl .type = str .help = The URL to which the cif and fcf file will be sent format = *pdf html .type = choice send = False .type = bool .help = If set to TRUE (default), the cif file will be sent to the checkcif url on pressing 'Validate Cif' } } image{ img_type = 'bitmap' .type= str label_symm = 'none' .type=str label_symm_type = 'default' .type=str trim_border_colour = #dedede .type = str bitmap{ AtomLabels{ font = '#olex2.fnt:frb_20' .type = str } BondLabels{ font = '#olex2.fnt:fr__14' .type = str } type = png .type = str resolution = 300 .type = int resolution_unit = in .type = str resolution_width= 4 .type = float size= 1200 .type = int transparent_background = False .type = bool trim = True .type = bool trim_border_colour = #bbbbbb .type = str trim_padding = 2 .type = float trim_border = 0 .type = float } ps { type = *eps .type = choice colour_line= " " .type = str colour_bond= " " .type = str colour_fill= " " .type = str perspective = " " .type = str outline_width = 1.0 .type = float octant_width = 1.0 .type = float pie_width = 0.6 .type = float octant_count = 5 .type = int octant_atoms = -C .type = str h_bond_width = 0.6 .type = float bond_width = 0.7 .type = float font_weight = 1.2 .type = float atom_label{ font_name = @ .type = str font_size = 15 .type = int font_colour = #00000 .type = colour font_weight = 1.0 .type = float } bond_label{ font_name = @ .type = str font_size = 8 .type = int font_colour = #00000 .type = colour font_weight = 1.0 .type = float } } } sorting { cat1 = "p" .type = str cat2 = "z" .type = str cat3 = "l" .type = str cat4 = "" .type = str moiety = "default" .type = str h = False .type = bool } modules { reference = "" .type = str location = "DataDir()" .type = str manual_update = False .type = bool provider_url = "https://secure.olexsys.org/PluginProvider1/" .type = str } NoSpherA2{ has_pyscf = False .type = bool enable_psi4 = False .type = bool enable_discamb = True .type = bool discamb_exe = "discambMATTS2tsc" .type = str salted_models_list = "" .type = str show_ri_fit = False .type = bool } Server{ host=localhost .type=str port=8899 .type=int debug=*None Wing VSC Eclipse .type=choice shared_localhost=False .type=bool } } odac .expert_level = 2 .short_caption = ODAC Settings { src_dir = None .type = path plugin_dir = None .type = path keyname = None .type = str is_active = False .type = bool debug{ debug = False .type = bool debug_deep1 = False .type = bool debug_deep2 = False .type = bool verbose = False .type = bool } version{ remote = "r41" .type = str } }