PEST 6.0 - TUNE - Isotropic simulations & optimizations


The TUNE program optimizes the values of simulation parameters to produce a calculated spectrum with minimum residual error as compared to the experimental spectrum. The text input_file contains experimental, simulation, and parameter output filenames, optimization settings and starting simulation parameters. TUNE can either be used to produce a single simulation or an optimized simulation. TUNE also has the AUTOSIMULATE function. This is used to pick out potential simulations from a very large set of possibilities for a single isotropic EPR spectrum, particularly those which display a a complex pattern of many lines.
Usage:  	tune filename

Esample:	tune testdata.tun

The filename "testdata.tun" refers to an ASCII parameter file which
contains all the information TUNE needs to execute.  The format of 
this file is displayed later in this document.  Information text will
be printed to the screen until notification that the program has
finished.  You can then examine the output files for results.

Creating the Input Files
Create the parameter and spectrum input files.  You can create the 
parameter file using either a text editor or by using functions
functions provided by both the  SimEPR  and  WinSIM 
programs.  You will need both a parameter (.tun) file and an
experimental spectrum file (.lmb, .exp, or .spc).  For instance:

	test01.tun		ASCII parameter file
	test01.lmb		binary experimental spectrum data file

Now run the program as a  command line program .


6.0.1	Format of the TUNE input file

The tune input-file is ASCII text and contains the following information: 
experimental file name, simulation file name, simulation parameters, 
optimization parameters.  All letters may be either upper-case or lower-case.  
The order of the parameters is generally insignificant.  All optimization 
flags are of the form 1= Optimize, 0= Remain Constant.  An example:

Tune input file.		unneeded title
----------------		unneeded divider
F0: 0				spectrum file types
F1: test01.lmb			experimental data file name
F2: test01.sim			simulation data file name
F3: test01.epr			text parameter output file
----------------
LMB fit parameters
HF: 1				Regular hcc analysis: 1= on, 0= off
PA: 0				Parametric hcc analysis: 1= on, 0= off
ST: 0				Step type: 0, 1, 2
NL: 7				Number of levels of iteration
----------------
Simplex fit parameters
RS: 4				Number of Restarts
IT: 600				Max iterations per restart
TL: 0.01000			Fractional Tolerance
----------------
Continuous wave fit range
DS: 1				Data start, low data point of CW fit range
DE: 4096			Data end, high data point of CW fit range
-----------------
Parameter constraints
CHF: 0, 10			hcc: 		flag, % deviation allowed
CLW: 0, 10			linewidt:	flag, % deviation allowed
CGS: 0, 10			g-shift:	flag, % deviation allowed
CRI: 0, 10			intensity:	flag, % deviation allowed
-----------------
Spectral parmaters
SM: 1				0=simple, 1=Nitroxide calculations
FT: 0				0=Continuous Wave, 1=Fourier
FF: 256				FT combined frequency, unneeded if FT=0
HA: 1				Harmonic: 0, 1, 2
MA: 1.333			Modulation amplitude in Gauss
TC: 0.5				ratio: time constant (ms) / scan time (s).
--------------
SP:  1				Species start identifier
LW: 0.100, 0			LW value, optimization flag
LS: 6.000, 1			Lineshape value, opt. flag
RI: 118.000, 1			Relative intensity, opt. flag
GS: -0.012, 1			G-shift value, opt. flag
NX: 16.0, 1			Nitroxide coupling
N1: 0.45, 1			Nitroxide low field linewidth
N2: 0.55, 1			Nitroxide mid field linewidth
N3: 0.65, 1			Nitroxide high field linewidth
aa: 0.718, 0.5, 1, 1		hcc value, spin, number, optimization flag
aa: 4.089, 0.5, 1, 1		''
aa: 5.270, 0.5, 3, 1		''
--------------			unneeded divider
SP:  2				species start identifier
LW: 0.100, 0			same as above...
LS: 0.000, 1
RI: 50.000, 1
GS: -0.037, 1
NX: 13.5, 1
N1: 0.67, 1
N2: 0.72, 1
aa: 0.54, 0.5, 3, 1
aa: 4.75, 0.5, 3, 1
aa: 0.556, 0.5, 1, 1

6.0.2	TUNE output

TUNE produces three output files, in our example:

test01.epr	ASCII text printout of simulation parameters
test01.out	ASCII parameter file wihch can again be used with TUNE
test01.sim	Simulation spectrum data file, same format as
		experimental data file
		
The text parameter output-file is a printout of the beginning and ending 
simulation parameters, SSR measurement, final Spearman's rank Correlation 
Coefficient, input and output filenames, and on the job time.  This 
file can be read on screen or output to a printer, perhaps using the 
Reporter program.  The simulation data output file can be loaded into 
the main EPR or WinSIM programs for viewing, comparing, and plotting.




6.1 - REPORTER - View and print text data files 

This is a small Microsoft Windows program to view and edit text files 
with the .EPR suffix, normally the output of TUNE.  In the MS-Windows 
properties box that accompanies each program icon, you should set the 
directory as the one most likely to contain these files.


Conversion to HTML by DRD. Jan, 1996