%PDB_Demo.m

% Demonstrate how we predict SAXS data from a PDB file.
%  Apomyoglobin structure stored in file, '1BVC.pdb'.
fname = '1BVC.pdb';
result = PDB_Geometry(fname); % assess scattering info.


%Structure result has lots of scattering info.
%key features are,
fprintf(1,'\nPredicted Excess Number of Electrons - %f.', result.Ne_excess);
fprintf(1,'\nPredicted Radius of Gyration = %f Angstroms.',result.Rg_contrast);

%Plot normalized SAXS pattern - I versus q.
figure(1); clf; semilogy(result.Ivq(:,1), result.Ivq(:,2));
xlabel('Q (A^{-1})'); ylabel('I (normalized Units)');
title('Normalized SAXS pattern');
axis([0 0.5 0.005 1.0]);

% Try to compute experimental signal.
Ne = result.Ne_excess; % Number of electrons per scatterer
C = 10/16700; % Concentration of protein is 10mg per ml with molecular weight of 16700 g/mol.
               % Thus this is a 0.0006 M solution
l = 0.002; % Pathlenth of X-rays through sample is 2mm
T = 0.1; % Only 10% of X-rays make it through the sample cell.
flux = 1e11; % X-rays per second incident on the sample.
time = 100; % Take a 100 second exposure.
ADUperXray = 1.5; % Pressume the ADU counts at the detector per x-ray is 1.5.
Spec_to_Phos = 800/0.087; % Distance from sample to detector in units of detector pixels.

scaled_data  = Rel_Scat(result.Ivq, Ne, C, l, T, flux, time, ADUperXray, Spec_to_Phos)
% Scaled data now has the Intensity at the detector as a function of q.

figure(2); plot(scaled_data(:,1), scaled_data(:,2));
xlabel('Q (A^{-1})');ylabel('I (ADUs per pixel)'); title('Computed Scattering from ApoMyoglobin');
axis([0 0.5 0 400]);