%------------------- LineShapeKin SETUP -----------------------------
%-- version 3.0
%
% 3/11/08
% Written by Evgenii Kovrigin, Medical College of Wisconsin
global YES NO ;
%% Read definitions of the fitting model from this file
model_setup;
% 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='../Data_for_MatLab';
%--- 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 = { 'Y92_x_w1', 'T70_x_w1', 'S123_x_w1', 'S123_x_w2', 'H12_x_w2'};
%resnames = { 'Y92_x_w1', 'S123_x_w1', 'S123_x_w2'};
%% 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
residue_number=4 ; %--- particular residue in 'resnames' to look at
% (read only in 'simulation', 'single' or 'just display data' mode)
%project_name= 'indiv' ; %- fit all of them individually to individual Koffs
%project_name= 'global';%- fit all of them to one Koff
% -- 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
%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 for fitting or simulation results
Stacked_Plot=YES; %--- YES to display the titration series stacked rather than overlayed
Percent_Shift=75 ; %-- percentage of the peak height for shifting next trace up. Applicable
% if Stacked_Plot=YES
% 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 -----