The operation of CD_Fit5 program is as easy as 1-2-3
1. Select a CD spectrum as the query file and then press the button of "plot".
The format of a query file is csv, with the first column
as
wavelength (unit :nm) and the second as CD signal. The two columns are
separated by a comma and the wavelength interval is
1nm. There are 3 formats for the CD signal depending on the choice
of data unit, which includes milli-degree, MRE (mean residue
ellitticity;deg.cm^2.dmol^-1), and delta-epsilon (M^-1.cm^-1). You can down load the examples of 3 different formats from BAS_mdeg.csv, BSA_MRE.csv, and BSA_dE.csv.
Besides the spectrum data, you also need to specify the
light-path (mm), protein concentration (mM), and number of amino acid
residues for further calculation.
2. Specify the parameters for matching then press the button of "Match Run"
There are 3 parameters need to be specified for "Match Run". The
first one is the
range of wavelength, in this program the wavelength range from 175
nm to 260 nm. The second parameter is the constraint of
protein concentration; the CD singal will need to
multiplye a factor to best fit a protein dataset.
If you are not sure the concentration of the query protein or you only
want
to match the shape of the CD curve, you can de-active the "Conc.
Constraint" by unchecking the box. The third one is dataset fixed,
the CD_Fit5 program compares all protein datasets and shows a
best-match file on the screen. If you want to use a specific dataset,
you can activate "Fixed-file" by checking the box. You can also up load a
user defined dataset into the program and for the format of the user-defined dataset, please refers to User_difine.csv.
3. Adjust the percentage for "Match/ MLR" and then press the button of "Fit_5"
Finally, you can adjsut the percentage of the match-file and the multiple-linear-regression of 4 structures (100% of alpha-helix; beta-strain; turn and coil). If the value of NRMS is big after "Match Run", the percentage for "Match/MLR" should be set a lower value.