##############################################################################
# The sNum section. Information belonging to the currently loaded structure
##############################################################################


snum
  .short_caption = Current Structure
  .caption = Settings that are saved with each structure
  {

  init
    .short_caption = Other Things
    .expert_level = 1
    {
    skip_history = False
      .type = bool
      .expert_level = 1
    }

  ccdc{
    note_to_staff = +++ Optional Note To Staff +++
      .type = str
    submission_type = +++ Please Choose +++
      .type = str
  }

  current_result{
    cif = None
      .type = path
    fcf = None
      .type = path
  }

  smtbx
    .short_caption = Solution & Refinement
    {
    inelastic_form_factor_table = *henke sasaki
      .type = choice
    atomic_form_factor_table = *it1992 wk1995 n_gaussian
      .type = choice
    }

  solution
    .short_caption = Structure Solution
    {
    program = ShelXS ShelXS86 XS 'olex2.solve' XM ShelXD SIR2008
      .type = choice
    method = 'Dual Space' 'Charge Flipping' 'Direct Methods' 'Patterson Method'
      .type = choice
    graphical_output = False
      .type = bool
    current_atomic_volume = None
      .type = float
    }

  refinement
    .short_caption = Structure Refinement
    {
    last_R1 = n/a
      .type = str
      .expert_level = 2
    graphical_output = False
      .type = bool
    program = ShelXL XL XH ShelXH XLMP ShelXL_ifc 'olex2.refine'
      .type = choice
    method = 'Least Squares' CGLS 'Gauss-Newton' 'Levenberg-Marquardt' \
      'Full Matrix'
    .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 = False
      .type = bool
      .help = Automatically update the weight instruction before the next \
        refinement
    suggested_weight = None
      .type = floats(size=2)
      .help = The weighting scheme parameters suggested by the refinement \
        program in a previous cycle
    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

    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 = False
        .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
    {
    bitmap
      .short_caption = png, jpg, bmp ...
      {
      name = None
        .type = str
      type = *png jpg bmp
        .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
      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
    }
  }

  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
    {
    date_collected = None
      .type = str
    crystal_image = None
      .type = str
    crystal_images_path = None
      .type = str
    crystal_mounting_method = None
      .type = str
    date_submitted = None
      .type = str
    operator = None
      .type = str
    submitter = None
      .type = str
    diffractometer = None
      .type = str
    title = None
      .type = path
    image = None
      .type = path
  }

  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
  }

  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 = False
      .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 = False
      .type = bool
    update_cif = False
      .type = bool
  }


  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
  has_recently_updated = 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
  eden_vis = False
    .type = bool
  void_vis = False
    .type = bool
  mask_vis = False
    .type = bool
  hover_buttons = True
    .type = bool
  portal_url = http://www.olex2.org
    .type = str
  portal_db_url = http://olex2.opencryst.net/content/DB
    .type = str
  checkcif{
    url = http://vm02.iucr.org/cgi-bin/checkcif.pl
      .type = str
      .help = The URL to which the cif file will be sent
    send = True
    .type = bool
      .help = If set to TRUE (default), the cif file will be sent to the checkcif url on pressing 'Validate Cif'
  }

  structurespace{
    url = http://www.olexsys.org:8092/structurespace/StructureSpace
      .type = str
  }

  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
    ccdc_mail = olex2-deposit@ccdc.cam.ac.uk
      .type = str
      .help = The email address to which the files will be forwared
    pop{
      name=ccdc
        .type = str
      htm = \etc\gui\blocks\templates\pop_ccdc_submit.htm
        .type = str
      width = 600
        .type = int
      height = automatic
        .type = str
      auto_height_constant = 310
        .type = int
      auto_height_line = 20
        .type = int
      position = center
        .type = str
      border = 10
        .type = int
    }
  }
}

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 = (254,150,50)
        .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./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 factor vs resolution"
      .help = "R1-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"
    }
    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%"
    }
  }
}

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
        }
      }
    }
  }

user
  .short_caption = User Specific
  {
  use_fader = 0.4
    .type = float
  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
  report_style = default
    .type = str
  report_template = default
    .type = str
  report_journal_style = rsc
    .type = str
  auto_refine_after_anis = True
    .type = bool
  ccdc{
    user_email = horst.puschmann@gmail.com
      .type = str
    ccdc_email = horst.puschmann@gmail.com
      .type = str
    portal_url = http://localhost:8080/structurespace/StructureSpace/ccdc_submit
      .type = str
    portal_username = ccdcsubmit
      .type = str
    portal_passwd = ccdcpass
      .type = str
  }
  cif{
    autorefine_if_no_cif_for_cifmerge = True
      .type = bool
    chckCif_output_format = *PDF htm
      .type = choice
  }
  image{
    bitmap{
      type = png
        .type = str
    }
  }
}

odac
  .expert_level = 2
  .short_caption = ODAC Settings
{
  source_dir = None
    .type = path
  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
  }
}