%------------------- 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.
%
% 3/29/08 - data localization changed
%-- Four parameter fitting but no changes made to here
% 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 results
results_path='results';
%-- Enter here a list of residues to use ----
% -- cut-and-paste them from Data_for_Matlab/matlab.peaklist ---
resnames = { 'V108_x_w1', 'S123_x_w1' };
w0_B = [ 7133.3 6.81070e+03 ];
residue_number=2 ; %--- 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 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 -----
%% Read definitions of the fitting model from this file
DPM_setup; %--- load DPM-specific parameters