!!! Beta Version !!!

Instructions for processing NH J-modulation data.

PART 1: Split fid and process spectra
PART 2: Peak picking and spectra assignment
PART 3: Data fitting and calculating RDC



PART 1: Split fid and process spectra

Required files:
		NH-jmod4edit.pl 	Processing script
		fid and procpar		Data
		nmrpipe			User must create an empty directory called nmrpipe

Step 1.1: 	Modify the output spectrum file name in line 303 of NH-jmod4edit.pl
		Replace 'ct' with protein name.
		Replace 'media' with the alignment media.
		Keep the '$k.lista.' part of the file name, the script will put the delay times into the file name.

Step 1.2:	Process the first spectrum for phasing.  The modulation delay parameter is called 'Delta'
		Run the script. Script_name.pl dir_name/ increment_param  (NOTE: the neccesity of the slash after the dir_name may be OS dependent)
		To run the script: ./NH-jmod4edit.pl nmrpipe/ Delta  (NOTE: the necessity of the dot-slash preceding the script name and the slash after the dir_name may be OS dependent)

Step 1.3:	Use nmrDraw to inspect the spectrum and obtain phasing values.
		Insert the correct phasing values in the ft2.com file.

Step 1.4:	Process all of the arrayed spectra.  This is done by adding spark at the end of the command.
		In this step, the script will extract the correct phasing value from ft2.com and apply it to all spectra.
		The script will also convert the spectra from nmrPipe format to Sparky format.
		To run the script: ./NH-jmod4edit.pl nmrpipe/ Delta spark



PART 2: Peak picking and assignment of spectra

Optional files:
		assign.pl 	Generic assignment script

Step 2.1:	Use Sparky for peak picking and spectra assignment.

Step 2.1.1:	If peak list is provided, use the 'rp' command to read in provided peak list for the 0.5 dataset.
		Adjust peaks and peak locations to match the J-mod data.
		
Step 2.1.2:	If the peak list is not provided, pick all of the peaks and use the 'lt' command to save the peak list.
		Assign each peak in the list as X# by running the script. Script_name.pl peak_list.list > placeholder.list
		To run the script: assign.pl 0.5.lista.ct-NHJmod_media.list > test.list
		Delete the peaks and read in the new peak list.
		Use the 'lt' command to save the new peak list with the assigned residues.

Step 2.2: 	Use the 'rp' command to read the peak list in for the other modulation spectra.
		Use the 'lt' command in Sparky to save the peak list including the data height (select this under the 'Options' for each dataset).
		Save the peak lists for all of the modulation spectra into the Data folder.



PART 3: Data fitting and calculating RDC

Required files (for NESG RDC, all of the files are in the Data directory):
		Peaklist				Sparky peaklist from Step 2.2.
		make_separate2.pl			This script combines data height from each modulation delay spectra into one file.	
		fitR.pl, fitR_1by1.pl, fitR_all.pl	Data fitting scripts.
		header-hsqc_ass.tab			Peaklist assignment header.
		hsqc_ass.tab				Initial peaklist without data height from Step 2.1, with a new header.
		iso.tab					fit file for the isotropic data from Step 3.2.
		align.tab				fit file for the aligned data from Step 3.2.
		i-jmod.tcl				RDC calculation script.
		Make sure that GNUPLOT is installed on your computer, the script should run in Fedora and Apple OS X (NOTE: if nmrpipe installed, must rename the gnuplot and gnuplot_x11 files in the nmrbin.linux and nmrbin.linux9 directories)

Step 3.1:	This script combines data height from each modulation delay spectra into one file.
		For NESG RDC datasets, 8 modulation delays are typically acquired.
		The delays are 0.5, 2, 3.5, 6.2, 7.3, 8.4, 12.5, and 14 ms.
			0.5.lista.tfr85a-NHjmod_phage.list
			2.lista.tfr85a-NHjmod_phage.list
			3.5.lista.tfr85a-NHjmod_phage.list
			6.2.lista.tfr85a-NHjmod_phage.list
			7.3.lista.tfr85a-NHjmod_phage.list
			8.4.lista.tfr85a-NHjmod_phage.list
			12.5.lista.tfr85a-NHjmod_phage.list
			14.lista.tfr85a-NHjmod_phage.list
		The make_separate2.pl script will gather the modulation delay times from the peaklist name,'0.5.lista.'
		An example of the data file:
		X100N-H.dat
			0.0005          1
			0.002           0.109761113747825
			0.0035          -0.748141116911881
			0.0062          -0.300806834361652
			0.0073          0.369656699889258
			0.0084          0.730327479829141
			0.0125          -0.54485049833887
			0.014           -0.48327796234773

		To run the script: ./make_separate2.pl

Step 3.2:	To run the fitting script:
		./fitR.pl                 Fit each residue individually.
		./fitR_1by1.pl            Fit all residues one by one.
		./fitR_all.pl             Fit all residues and output the data into 'fit' file.
		
		The fitting of each residues can be inspected by running the fitR_1by1.pl.
		NOTE: The fitting script will append subsequent fits to the end of the existing fit file. You must delete the file and then run the fit to obtain the final fitting file.

Step 3.3:	The RDC can be calculated by subtracting the isotropic J and aligned J+D values in the fit file. (NOTE: Care must be taken to modify script based on any change in the signs of the gyromagnetic ratios of the two nuclei, the script is by default set up for N-H (N-C is also ok, since C and H both have positive gyromagnetic ratios)

		First, remove the Sparky header from the initial peaklist.
		To reformat the initial peaklist with the correct header: cat header-hsqc_ass.tab ~/dir_path/0.5.lista.ct-NHjmod_media.list > hsqc_ass.tab
		Rename the isotropic and aligned fit files as iso.tab and align.tab, respectively, and move to the RDC-Calculation directory.
		To run the RDC calculation script: ./i-jmod.tcl