##############################################################################
# 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
    }

  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
  }


  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
      .type = choice
    atomic_form_factor_table = *it1992 wk1995 n_gaussian
      .type = choice
    secondary_ch2_angle = idealise refine *shelxl
      .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
    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
    goof = None
      .type = float
    flack_str = None
      .type = str
    hooft_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 = ShelXL_ifc XL XH ShelXH-1997 XLMP ShelXL ShelXL-1997 '*olex2.refine' \
      Tonto Unknown  ShelXL-2012 ShelXLMP-2012 ShelXL-2013
      .type = choice
    method = 'Least Squares' CGLS '*Gauss-Newton' 'Levenberg-Marquardt' \
      'Full Matrix' HAR 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
    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
    original_formula = None
      .type = str
      .expert_level = 1
    use_solvent_mask = False
      .type = bool
    recompute_mask_before_refinement = False
      .type = bool
    check_absolute_structure_after_refinement = True
      .type = bool
    cifmerge_after_refinement = 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
      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
      }
  }

  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
    cif_od_file = None
      .type = path
      .expert_level = 1
    crystal_image_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_cif_od_files = None
      .type = strings
      .expert_level = 2
    list_crystal_images_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
    crystal_images = None
      .type = strings
    crystal_image = None
      .type = str
    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
      .type = choice
    type = *diff fcalc tomc fobs
      .type = choice
    mask = True
      .type = bool
    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
  }

  cif {
    htab_max_d = 2.9
      .type = float
    htab_min_angle = 120
      .type = float
  }

  olex_conres = RRINGS
    .type = str
  refinement_banner_slide = 82
    .type = int
}

olex2
  .short_caption = Olex2 Internal Settings
{
  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
  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

  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
    }
  }
  executable_check
   .help = "Instructs to check the particular file is executable on non-Win platforms"
  {
    pyl = 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
  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_acta_stuff = False
    .type = bool
  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
  start_where = home
    .type = str
  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
  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
  }

  graphs
    .short_caption = Analysis Graphs
    {
    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
      }
      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"
      }
      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 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{

      flack_str{
        display = "Flack"
          .type = str
        href = "spy.make_reflection_graph(wilson_plot)>>spy.make_reflection_graph(cumulative_intensity)"
          .type = str
        target = "Flack 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 = 0.82
          .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 = "R<sub>int</sub>"
          .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 = "complete"
          .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 = HklStat
          .type = str
        resolution = max *full
           .type = choice
        target = "Show reflection statistics - hkl file must be present"
          .type = str
      }
    }
  }

  diagnostics{
    pin_scopes = True
      .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
   }

  }
  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
  }
}

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
  }
}