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First you will need to set up a mechanism. This can be done with a text
editor such as Windows notepad. If you use a word processing program such
as MS Word, you must save the mechanism in a text format.
Example of a mechanism:
E + S == ES == EP == E + P
where the double equals sign,==, defines a
reversible step governed by forward and reverse rate constants. (A single
equals sign, =, defines a step governed by a dissociation constant).
Follow the mechanism equations by an *OUTPUT and the desired output
equations. example:
E + S == ES == EP == E + P *OUTPUT F1*S F2*(ES + EP)
where F1 and F2 are just factors to convert observed results from
concentrations to, for example, absorbance. In this example S and (ES +
EP) will be displayed as
separate lines on the graphical output when the factors are nonzero.
Mathematical operators that can be used in the output expressions are ^
(exponential), * (multiplication), /
(division), + (addition), - (subtraction) and % (logarithm). A $ or ! are
for remarks should you wish to include them. A [1 holds the concentration
of a species (e.g., S[1) constant.
Species names can be complex. For example AA or A2 is a dimer of
A, 2AB3O4 is 2 molecules each with 1A, 3B's and 4 O's.
Save the file you have created as filename.mec
Run KINSIM40.EXE by clicking on it and a menu will appear. You will find
an instruction (O) that allows you to compile the
filename.mec file to a .sim file necessary for running KINSIM. After
compiling the mechanism, choose M and load the simulation
file,
filename.sim.
From the menu, choose C to enter concentrations. Control E
(followed by a return or enter) always returns you to the menu. Choose K to put in the rate constants Choose F to put in factors Choose T to put in values of delta time
run time Ymax Flux tolerance (default = .02) Integral tolerance (default = 1E-3)
Be sure
that concentrations, rate constants and run time have consistent
units. Again, Control E (return) will take you out of the window and back to the menu.
Delta time requires some explanation. You
can put in a relatively large value (like 1) and the program searches for
the smallest delta time that falls within an integral tolerance range. If
you
start with a very small value (1e-5), and your data covers a long
time, the program may take a long time to simulate. Therefore,
unless the
program crashes, it is best to use a relatively large value. The
integrations will define how many points are in the simulated plot. For
example, if delta time is 1 and integrations is 1 and the runtime is 100
sec, there will be 100 points. If the integrations is set to 5, there will
be 20 observed points on the graph and so on.
Once you have performed a simulation to your liking, you can
save values of all the parameters for rate constants, concentrations etc.,
by choosing S. This will create a *.sav file. You can restore these
values by choosing R and typing in the name of the .sav set when
asked. The .sav files will be used for FITSIM.
P will change the background color of the
graphics between black and white.
L lets you output the simulation into a file which then can be ported
to a spread sheet.
To run, choose G. Nothing (except some blinking) will happen until
the simulation is finished.
To load real data files.
Real data files must be in the proper format. Since every instrument
produces a different ASCII file, you will need to convert that file
to one that is appropriate. Once you have downloaded the real data ASCII
file from your equipment to the proper folder, choose A to convert
the ASCII file to the required *.rdf file. Follow the directions indicated
to do the conversion. You will need to know the lines for the first and
last data points and you should be able to get these from the screen
display. While this program works well, it is possible that the conversion
program will not be completely universal. Should you need to convert
an ASCII file, the structure should be two columns (time, data) with no
headers or footers. In this case the data must be saved as a text
file.
If you wish to include the real data you have converted as background for
the simulation, choose I. You may load up to 20 data files. A
screen will show you the parameters. Once the data are accepted the
runtime and Ymax for the last file chosen will be inserted automatically
into the KINSIM program under T (see above). To remove the data
file(s), type I again. New data files can then be
loaded.
There is a more complete manual. Documentation is currently available from
wuarchive.wustl.edu/kinsim/packages/docs.w51 is documentation written in
Word 5.1. The documentation is extensive but slightly different from the
program you are using since it was written for the original VAX
programs. |
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You need to have one .sim file and a .sav set for every data set you
fit. The .sav set is created from KINSM for each data set. FITSIM globally
fits many data sets and is fairly self-explanatory. Start by clicking on
FITSIM40.EXE to run the program.
Choose (1) to make a *.fdt file for fitting. The default is
autosim.ftd but you can use other names. Choose (2) to start the fitting. You will be provided with a series of options.
In a complex mechanism it is best to hold as many rate constants as
possible constant allowing just a few to float. The
limits of the varied rate constants are set very large and can be
decreased without harm. For the most part you can just use default
values for everything else. The simulation of the data (.rdf file) to
create the .sav sets must have exactly
the same runtimes. If you wish to change the runtime you must do it
in the ASCII data file and create a new .rdf file. This new version of
FITSIM contains several new features. These include the ability to fit
data with uneven as well as fixed time points, the ability to fit any of
several outputs, the ability to simultaneously view up to 20
different real data files and the ability to float the factors, in
addition to rate constants, in the mechanism.
Choose (3) to view the fitted curves to the real data
(assuming the fitting was successful).
ASCII files (*.ftd) of the
fitted curves are generated after the fitting is complete. These files can
be exported to any spreadsheet or graphics program for
making publication quality plots. ASCII files (*.dxy) of the real data are
also generated in KINSIM40.EXE during the file conversion and are useful
if the original ASCII data were transformed. |
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For KINSIM:
For FITSIM:
see also
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