The server displays the profile fit along with the residuals ((experimental-computed)/error) on the
left side of the window. The input structure is displayed in a JSmol window.
The input experimental profile is shown with black dots, while the
theoretical profile is a red line.
The user can zoom on different parts of the fit plot, rotate the structure in the JSmol window, and
use show/hide button to display or hide the computed profile and the corresponding structure.
The file with the theoretical profile fitted to the experimental one can be downloaded using the
link under the plot. The format of the fit file is the same as the input profile files,
with additional column added that included the calculated profile.
The quality of the fit, χ2 value, is printed below the plot.
There are 2 free parameters in profile fitting:
(i) c1 - is the scaling of the atomic radius and it controls the exluded volume of the molecule
The default value is c1 = 1.0. During fitting, we allow up to 1% decrease in the radius and up to 5% increase (0.99 ≤ c1 ≤ 1.05).
(ii) c2 - is used to adjust the difference between the densities of the hydration layer and the bulk water.
This parameter controls the density of the water layer around the molecule.
The default value is c2 = 0.0. During fitting, the value of c2
can vary from 0 to 4.0, reflecting an estimate of up to four water molecule neighbors for an exposed
solute atom. This threshold is comparable to the average number of water
molecules within 3Å of each other in the TIP3P water box. The hydration
shell density for c2 = 4.0 is 0.388e/Å3.
The density of the hydration layer around the protein can, in principle, be lower than that of bulk water,
depending on the amount of surface charge. Therefore, we also allow c2
to be slightly negative (-2.0 ≤ c2 ≤ 4.0).
The hydration shell density for c2 = -2.0 is 0.307e/Å3.
Given experimental profile,
FoXS finds a combination of c1 and c2 that achieves the best fit
(lowest χ2 value) to the experimental data.
Extreme values of c1 and c2 parameters often indicate data overfitting.
For example, if you have missing residues in the structure, FoXS can compensate for the missing
electron density by increasing the hydration layer density by setting c2 parameter to the maximal value of 4.0.
These values are flagged by FoXS in the results table to alert the users of possible overfitting.