XSPEC-SIM Read Me

This program allows for the simulation of the NEXAFS spectrum of proteins and peptides at the Carbon, Nitrogen, and Oxygen edges.

To simulate a protein or peptide spectrum:
1)Write the protein sequence using single letter amino acid codes into the main text box.
2)Write the protein name into the smaller textbox at the bottom of the IDL window.
3)Check or UnCheck the checkbox in the bottom right labeled "Save SF".  If this text box is selected the elemental response of the protein/peptide will also be calculated and saved.
4)Select the desired edge of the output data in the first dropdown box (Carbon, Nitrogen, Oxygen, or CNO are in the default data files).
5)Select the data set to use -- for most purposes the default "20AA_OD1" works well.  This dataset is based on the amino acid spectrums reported by Zubavichus et al. and was converted to the OD1 scale (ie normalized to the computed elemental response of 1 nm of the proteins chemical composition) by Jacob Stewart-Ornstein.
6)Click on Either "Uncorrected Spec" or "Peptide Bond Corrected"
	-Uncorrected Spec: returns a weighted sum of the amino acid spectrums present in the peptide/protein normalized into a OD1 scale
	-Peptide Bond Corrected: takes the weighted sum and adds in the spectrum of the peptide bond (calculated by comparing amino acids to their di-and-tri-peptide equivilents.  This is recomended for most purposes as it corrects significant errors involving the locations of the Amide/Carboxylic peak in the protein spectrum.
7)save the resulting files, which can be read as text files by axis.