%------------------- LineShapeKin SETUP ----------------------------- %-- version 1.1 % % 3/21/08 % Written by Evgenii Kovrigin, Medical College of Wisconsin % % 3/22/08 - interfaced to Direct Parameter Mapping % 3/25/08 - bugs fixed. % NOTE: This 'setup.m' is STRICTLY SPECIFIC for a three-parameter model % where we fit Kd, Koff and w0_B with w0_B individual for every % residue. It is taken from corresponding array as a starting % value for fitting. Here you CANNOT use GLOBAL fitting mode global YES NO ; % Define enzyme concentration at each titration point. If your addition of % ligand did not change volume - use the same number for all points Ptotal = [ 530 530 530 530 530 530 530 530 530 530]*1.0e-6; % M % Total Ligand/Protein ratio at each titration point LPratio = [ 0 0.0812 0.162 0.325 0.487 0.649 0.812 0.974 1.14 1.3]; %-- Temperatures (only used with temperature-dependent model. Otherwise - % ignored. T = ones(1,length(Ptotal)) *298; % NOTE: If you need to exclude any points for a SPECIFIC residue from % fitting (due to overlap) - edit 'titration_points.txt' file in the % residue data folder. %--- Path do Sparky data folder %Sparky_data_path='/Users/kovrigin/Documents/Workspace/Data/Data.XI/EKM7.LINESHAPEKIN_for_ENC_2008/Version_3.0/User_Data/DPM.Kd_koff_v0/Data_for_MatLab/'; Sparky_data_path=''; %--- Folder where to save pictures figures_path='figures'; %-- Enter here a list of residues to use ---- % -- cut-and-paste them from Data_for_Matlab/matlab.peaklist --- resnames = { 'V108_x_w1', 'H12_x_w2', 'Y92_x_w1'}; w0_B = [ 7133.3 4.73661e+03 8.04177e+03 ]; residue_number=1 ; %--- particular residue in 'resnames' to look at % (read only in 'simulation', 'single', 'just display data' and 'Direct Parameter Mapping' mode) %% --- MODE OF OPERATION --- %project_name='simulation'; %-- calculate titration profile using provided R2 and w0 values %project_name='just display data'; %- only do normalization and plotting of raw data project_name= 'single'; %- lets you fit just one of them % in this case set residue_number=... desired number % in all other cases this % variable is disregarded %project_name= 'individual' ; %- fit all of them individually to individual Koffs %project_name= 'global';%- fit all of them to one Koff %project_name= 'DPM'; %--- direct parameter mapping mode %% ===== DIRECT PARAMETER MAPPING modes --- DPM_session='single'; %--- single residue calculation %DPM_session= 'individual'; %--- calculation calculations on the entire set of % residues. %-- Choose mode of DPM operation (these modes are used consequtively % for convenience because 'computation' is run only once and takes a % long time, while 'analysis' is fast and may need to be rerun multiple % times with different SSD levels (see DPM_setup.m) %DPM_mode='computation'; % computation of SSD matrices DPM_mode='analysis'; % analysis: selection of equivalent parameter sets and plotting %==== END OF DIRECT PARAMETER MAPPING SETTINGS ==== %% THIS SECTION IS SPECIFIC TO A 'SINGLE' FITTING SESSION FOR A MODEL ADJUSTING W0_B % these are the starting values of w0_B % you must first determine in 'just_display_data' runs Model.w0_B = w0_B(residue_number); model_setup; %-- to set up limits for this parameter % -- Normalization by total integral of the trace: % It requires that peak tails go down to baseline ON BOTH SIDES, % otherwise incorrect results will be obtained: first and last points of the trace are taken as % constant baseline estimate to subtract baseline. Normalization='integration' ; %Integration_mode='rectangular'; %-- integration by rectangular formula Integration_mode='simpson'; %-- integration by Simpson's formula NOTE: % 2. ---- Baseline correction --- % Use ONLY when your peak falls off to the noise floor AT LEAST on one % side and noise floor is elevated %Baseline_Correction=YES; Baseline_Correction=NO; % 3. --- starting line width in fitting of initial raw data for % determination of positions and relaxation rates of end points Line_Width_0=50; % -- Plotting option Stacked_Plot=YES; %--- YES to display the titration series stacked rather than overlayed Percent_Shift=10; %-- percentage of the peak height for shifting next trace up. Applicable % 5. -- Before starting, make sure that Matlab knows where the code is: % use File:Set Path and [Add Folder] % 6. ---- NOW YOU ARE READY. TYPE IN 'main' AT A MATLAB COMMAND LINE ----- %% Read definitions of the fitting model from this file DPM_setup; %--- load DPM-specific parameters