####################################################### # System defaults file for orbplus ####################################################### # # Specify the program for opening the help files included in the software # This can be a favorite browser or "open" in macosx. #*browser: open # # Specify the location of the pymol program #*pymol_prog: /usr/local/bin/pymol ####################################################### # Inputs ####################################################### # # Set default location of database index file. #*db_index_file: # # Set default location of input protein file. #*input_file: # # Indicate the chemical shift atoms we are interested in. #*atomNameX: H HN #*atomNameY: N # # If the atoms specified above have significantly different ranges of values # then indicate a bias or scaling factor that will equalize calculations involving # the shift change. For example, protons shifts are about 5 times less than # nitrogen shifts so a ybias of 0.20 will dampen the nitrogen shift change. #*yBias: 0.20 ####################################################### # pymol defaults ####################################################### # # Set default location of pdb file to use with pymol #*pymol_pdb_file: # # Dimensions and location of pymol window #*pymol_geometry: 600x500+565+30 # # un-selected color of residues #*pymol_bgcolor: green # # selected color of residues #*pymol_selectcolor: red # # default init pymol commands #*pymol_init: hide lines ; show cartoon ####################################################### # Prediction Calculation ####################################################### # # Top number of residues to use in prediction #*topres: 10 # # Specify weighting factors for each prediction term. # The default is set them all to one which means all the terms are weighted the same. # # How important is it to chose the residues in the database that have largest shift? #*dis0_db_weight: 1 # # How important is it to chose residues that have the largest shifts in the input data? #*dis0_inp_weight: 1 # # The importance of selecting residues where shift change is the same direction #*theta_weight: 1 # # The importance of choosing residues where the database variance is low. #*var0_weight: 1 # # What score do we give for database variance if there is only one data point? # Enter "end" to indicate all residues with > 1 data point have a higher score. # Enter "average" to use the average score (eg, minimize the penalty) # Or enter the number of the score that you believe appropriate for your case. #*no_variance: end ####################################################### # Output ####################################################### # # Default place to write output #*write_dir: # # This is where we write the per residue calculations table #*out_calc: calc.txt ####################################################### # Main window ####################################################### # # geometry (just specify location of the window) #*main_geometry: +80+25 # # set font in calculation results window #*textwin_font: -*-courier-medium-r-normal--12-*-*-*-m-*-iso8859-1 #*textwin_ht: 15 #*textwin_wd: 58 # # Customize the residue selection tableau #*col_max: 10 #*colWidth: 5 #*rowWidth: 2 #*r_border: 10 #*no_select_color: grey60 #*ignore_color: grey90 #*select_color: red # # bg color for entry boxes *entry.background: yellow ####################################################### # Calculations window ####################################################### #*wpredict_geometry: ####################################################### # Spectra window 0: All peaks # These settings are applicable for the other plots as well ####################################################### #*canvas_win_title_0: residue-all #*canvas_label_text1_0: #*canvas_label_color_0: black #*canvas_label_x_offset_0: 0 #*canvas_label_y_offset_0: -25 #*canvas_geometry_0: 450x325+565+25 #*canvas_bg_color_0: beige #*canvas_font_0: -*-times-medium-r-normal--12-*-*-*-m-*-iso8859-1 # #*axis_color_0: blue #*db_symbol_0: oval #*db_symbol_size_0: 5 #*db_ref_color_0: red #*db_select_color_0: black #*db_noselect_color_0: pink #*vector_flag_0: no #*vector_color_0: black #*db_unhilite_color_0: grey #*data_symbol_0: cross #*data_symbol_size_0: 3 #*data_input_color_0: black #*data_title_0: Input #*margin_left_0: 60 #*margin_bottom_0: 40 #*margin_top_0: 40 #*margin_right_0: 30 # #*x_label_text_0: Hn(ppm) #*x_label_color_0: blue #*x_label_x_offset_0: 0 #*x_label_y_offset_0: 30 #*x_tics_0: 8 #*x_format_0: %5.3g # #*y_label_text_0: N(ppm) #*y_label_color_0: blue #*y_label_x_offset_0: 10 #*y_label_y_offset_0: 20 #*y_tics_0: 8 #*y_format_0: %5.1f ####################################################### # Spectra window 1: Expanded spectra specific residue ####################################################### #*canvas_win_title_1: residue-expand # ####################################################### # Spectra window 2: Multiple spectra specified residues ####################################################### #*canvas_win_title_2: multiple-res-plot # # possible settings for compact spectra #*canvas_font_2: -*-courier-medium-r-normal--10-*-*-*-m-*-iso8859-1 #*x_label_text_2: #*y_label_text_2: #*vector_flag_2: no #*x_tics_2: 3 #*y_tics_2: 3 #*db_symbol_size_2: 3 #*data_symbol_size_2: 3 #*margin_left_2: 40 #*margin_bottom_2: 20 #*margin_top_2: 20 #*margin_right_2: 20 ####################################################### # Spectra window 3: Histogram ####################################################### *canvas_win_title_3: Shift Change Summary #*canvas_geometry_3: 903x493+565+375 # # histogram title lines, if commented out, use software defaults #*canvas_label_text1_3: #*canvas_label_text2_3: #*canvas_label_color_3: black #*canvas_label_x_offset_3: 0 #*canvas_label_y_offset_3: -25 # # x-scale #*x_label_text_3: Residue #*x_label_color_3: blue #*x_value_start_3: 5 #*x_value_incr_3: 5 #*x_axis_min_3: #*x_axis_max_3: #*x_label_x_offset_3: -20 #*x_format_3: %.3g # # y-scale #*y_label_text_3: Shift(ppm) #*y_label_color_3: blue #*y_tics_3: 11 #*y_axis_min_3: #*y_axis_max_3: #*y_label_x_offset_3: -20 #*y_label_y_offset_3: 15 #*y_format_3: %4.1f # # Colors and sizes(in pixels) for the various histogram bars #*xScaleOffset_3: 20 #*linecolor1_3: blue #*linesize1_3: 10 #*linecolor2_3: red #*linesize2_3: 6 #*linecolor3_3: pink #*linesize3_3: 2 #*linecolor4_3: black #*linesize4_3: 2