# ####################################################### # 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 ####################################################### # Output ####################################################### # Default place to write output *write_dir: # This is where we write the per residue calculations table *out_calc: calc.out ####################################################### # Prediction Calculation ####################################################### # 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 ####################################################### # 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 ####################################################### # Window attributes ####################################################### ####################################################### # Main window # geometry (just specify location of the window) *main_geometry: +50+25 # set font in calculation results window *textwin_font: -*-courier-medium-r-normal--12-*-*-*-m-*-iso8859-1 ####################################################### # Spectra: All peaks *canvas_geometry_0: 450x325+565+25 *canvas_bg_color_0: beige *canvas_font_0: *axis_color_0: *db_symbol_0: oval *db_symbol_size_0: 5 *db_unhilite_color_0: grey *db_state1_color_0: red *db_state2_color_0: black *vector_flag_0: no *vector_color_0: black *data_symbol_0: cross *data_symbol_size_0: 3 *data_input_color_0: black *data_title_0: Input ####################################################### # Spectra: Expanded at specific residue *canvas_geometry_1: 450x325+1018+25 *canvas_bg_color_1: beige *canvas_font_1: *axis_color_1: *db_symbol_1: oval *db_symbol_size_1: 5 *db_unhilite_color_1: grey *db_state1_color_1: red *db_state2_color_1: black *vector_flag_1: no *vector_color_1: black *data_symbol_1: cross *data_symbol_size_1: 3 *data_input_color_1: black *data_title_1: Input ####################################################### # Spectra: Multiple spectra at specified residues *canvas_geometry_2: 900x500+570+280 *canvas_bg_color_2: beige *canvas_font_2: *axis_color_2: *db_symbol_2: oval *db_symbol_size_2: 5 *db_unhilite_color_2: grey *db_state1_color_2: red *db_state2_color_2: black *vector_flag_2: yes *vector_color_2: black *data_symbol_2: cross *data_symbol_size_2: 3 *data_input_color_2: black *data_title_2: Input ####################################################### # Histogram # window dimensions *canvas_geometry_4: 903x493+565+375 *canvas_bg_color_4: beige *canvas_font_4: # Margins *margin_left_4: 70 *margin_bottom_4: 50 *margin_top_4: 30 *margin_right_4: 50 # Number of tic marks for x and y scale *y_tics_4: 10 *x_tics_4: 30 # Colors and sizes(in pixels) for the various histogram bars *linecolor1_4: blue *linesize1_4: 10 *linecolor2_4: red *linesize2_4: 6 *linecolor3_4: pink *linesize3_4: 2 *linecolor4_4: black *linesize4_4: 2 # Others *graph_label_text_4: *graph_label_color_4: black *graph_label_x_offset_4: 0 *graph_label_y_offset_4: -25 *x_label_text_4: "" *y_label_text_4: "" *x_label_color_4: blue *y_label_color_4: blue *x_label_x_offset_4: 0 *x_label_y_offset_4: 30 *y_label_x_offset_4: 10 *y_label_y_offset_4: 20 *x_format_4: "5.2f" *y_format_4: "5.1f"