Create a directory for running your experiments (e.g. <ADAPT_NMR_on_my_protein>).
Copy the parameters.txt, nmrpipe.par, ORTHO_list.txt, ADAPT_list.txt files from the ~/vnmrsys/adapt_nmr/input_files 
directory to the <ADAPT_NMR_on_my_protein> directory you just created (also copy a text file with the sequence for 
your protein).  Update the parameters.txt file according to input_files.README file.


Calibrate pw/tof for your protein sample and save the values in the probefile.


####################################################################
running ADAPT_ORTHO to collect and process orthogonal planes
####################################################################

In vnmrJ, run quick 2D experiments to establish spectral window and offset in the indirect dimension 
for:

N15 (run N15-HSQC, use sw1, dof2 for N15-HSQC)
CO  (run HNCO, use sw1, dof for HNCO HNCACO)
CA  (run HNCA, use sw1, dof for HNCA HNCOCA)
CB  (run CBCACONH, use sw1, dof for CBCACONH, HNCB)

NOTE: do NOT make the spectral window in the indirect dimension too tight or the peaks may fold in 
the tilted planes


Edit ORTHO_list.txt file:
	 Enter the sw1, dof/dof2 values calibrated above (replace values given in the example input file).


Edit nmrpipe.par file:
	
	From quick HNCO above, set parameters for extracting the amide region in the direct dimension for 
	nmrpipe processing (remember that the values are in points and the final total size for the direct 
	dimension is 2048). Enter these into the nmrpipe.par file.

	Apart from the N15-HSQC, for all other experiments the phasing parameters for the direct proton dimension 
	should be identical, so you can just enter the rp value (lp should be zero) you get from the quick 2D HNCO 
	your ran above into the nmrpipe.par file


Go to vnmrj, cd into the <ADAPT_NMR_on_my_protein> directory and type ADAPT_ORTHO.
	All orthogonal planes listed in ORTHO_list.txt will be automatically collected and processed
	(you can look at spectra in vnmrj as they are being collected, but don't change experiment or quit 
	vnmrj or you'll interrupt the run).

 	If you need to adjust parameters and reprocess some of the spectra, edit the "ft_ortho.com" file
	that is saved with each experiment and run the "run_nmrpipe" macro to reprocess each spectrum
	NOTE. The processing parameters from the 0 degree orthogonal plane will be used to process the 
	tilted planes.

	
Once all orthogonal planes are collected and processed properly, you are ready to run ADAPT_NMR


###################################
running ADAPT_NMR 
###################################

Edit ADAPT_list.txt file (very similar to ORTHO_list.txt)

Type ADAPT_NMR in vnmrj command line and let the spectrometer and computer do their work !!

At the end, the results should be located inside the output_files directory.