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Scripts are a useful way to use pynmr.  Instead of using 
the GUI, you can list commands in a script file and then 
run that file.

-------------------IMPORTANT-----------------------------

The first line of your script file should always be:

import pmg_tk.startup.pynmr.nmr_cmd as nmr_cmd

-------------------RUNNING--------------------------------

To run your script file, in the pymol text window type:
run myscript
You do NOT need execute permission on your script file.

-------------------COMMANDS--------------------------------
 startpynmr
 -> opens up the pynmr gui

 superimpose(ref, atoms, range, bbdef, pairfit=0, \
 	progressflag=0):
 -> superimpose, writing rmsds to the screen

 C_do_best_range(ref, atoms, bbdef, string_of_objects, \
    range, workingdir, stop_rmsd)
 -> find the best range to superimpose on.
    (sorry, it's rather long to enter the entire 
	string_of_objects but there is no other way)

 show_bbonly():
 -> turns on backbone-only viewing

 load_file(list_file)
 -> loads all files which are listed in the given file.

 load_models(bigfile)
 -> load in bigfile, which contains multiple structures

 load_root(rootname, first, last)
 -> loads a bunch of pdb files with the same rootname,
    in the range first-last.

-------------------EXAMPLE---------------------------------
import pmg_tk.startup.pynmr.nmr_cmd as nmr_cmd
nmr_cmd.startpynmr()
nmr_cmd.load_root("aria_", 1, 25)
nmr_cmd.show_bbonly()
nmr_cmd.superimpose('aria_1', 'C N CA', 'all', 'C N CA', \
        pairfit=0)
nmr_cmd.C_do_best_range('aria_1', 'C N CA', \
        "aria_1 aria_2 aria_3", "all", \
		"/home2/leigh/Proj/py/data1", 1.0)
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