XSpecSim 
^^^^^^^^
Author: Jacob Stewart-Ornstein
file:  XSpecSim-ReadMe.txt
last changed:  19-July-2010  (aph)

If data generated by XSpecSim are used ina scientific publication please cite

J. Stewart-Ornstein, A.P. Hitchcock, Daniel Hernāndez-Cruz, P. Henklein, J. Overhage, K. Hilpert, J. Hale and R.E.W. Hancock,  Using intrinsic X-ray absorption spectral differences to identify and map peptides and proteins, J. Phys. Chem. B 111 (2007) 7691-7699. 

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DESCRIPTION OF XSpecSim and how to use it
-------------
This program simulates the NEXAFS spectra of proteins and peptides at the Carbon, Nitrogen, and Oxygen edges. The structure of the code was written with the intent to allow later extension to smulating the spectra of any polymer constructed from a small number of repeating units for which reference NEXAFS spectra might be available, such as nucleotide sequences (DNA, RNA); polysaccharides, and block co-polymers.

To simulate a protein or peptide spectrum:
-----------------
1)Write the protein or peptide sequence using the single letter amino acid codes into the main text box.

2)Write the protei / peptide name 

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 (all 3 edges) are 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 spectra reported by Yan Zubavichus,Andrey Shaporenko, Michael Grunze and Michael Zharnikov, J. Phys. Chem A (Letters) 109, 2005, 6998-7000.
Each of those 60 spectra were 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)Generate the simulated spectrum by clicking on either
 	- "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.

each of the two commands displays the simulated spectra and asks the user to provide a location and name to save the resulting files

7) When finished, close the widget with 'Dismiss'

Note the similated sepctra can be read into aXis2000 or other spectral display programs..


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XSpecSim CODE files
============================

These are the files that together, construct the
XSpecSim widget in aXis2000

AA_WriteConfig.pro
AverageVal.pro
extrapolateaa.pro
genextrap.pro
GetPath.pro
length.pro
ParseComposition.pro
ReadData.pro
read_AAdata.pro
read_AA_header.pro
read_energies.pro
Regress2.pro
sav_AA.pro
SFConvert.pro
XSpecSim-ReadMe.txt
xspecsim.prj
xspecsim.pro
xspecsim_com.pro
xspecsim_init.pro
xspecsim_run.pro
XspecSm.lst
XSpec_ReadMe.txt

Programming Notes
------------------
If you make a SAV file from this set of files
the result does not work as it needs to start with XSpecSim_run
which initializes the energy and amino acid parsing

This same set of files are now (as of 19-Jul-2010) in 
aXis2000 so that it is compiled on the fly.

-------------------
If you want to run the peptide / protein spectral 
predictor package outside of aXis2000
and you have a licensed version of IDL

Type  XSpecSim_run in the command line

It is possible you may need to run aXis2000 first, stop it
then run this command, in order to set up the X-ray absorption
cross-section tabulation system (SF)
