Small-Angle X-Ray Profile

q = (4πsinθ) / λ

2θ is the scattering angle, λ the incident wavelength

Small-Angle X-Ray Profile calculates a theoretical small-angle X-ray scattering (SAXS) profile from a set of atoms. The result can be displayed along with an experimental profile provided by the user. Calculations are performed with the program FoXS,

FoXS: a web server for rapid computation and fitting of SAXS profiles. Schneidman-Duhovny D, Hammel M, Sali A. Nucleic Acids Res. 2010 Jul 1;38 Suppl:W540-4.

There are several ways to start Small-Angle X-Ray Profile, a tool in the Higher-Order Structure category.

The Molecule setting controls which atoms will be included in the calculation:

• any one of the open molecule models
• all molecules - all molecule models combined
• selected atoms - the currently selected atoms

Optionally, an Experimental profile can be read from a file. If an experimental profile is provided, the theoretical profile will be scaled to fit the data. The file should contain an initial comment line followed by three whitespace-preceded columns: q value, measured scattering, and measured scattering error (see an example file for lysozyme). The error values are used for fitting but are not plotted.

For comparison to experimental data, the structure should be as similar as possible to the experimental sample in terms of which atoms are present (not missing domains, loops, or parts of residues). Dock Prep can be used to repair truncated side chains and/or add explicit hydrogens.

Clicking Options reveals additional settings (clicking the close button on the right hides them again):

• Excluded volume adjustment (on by default) - whether to adjust the excluded volume parameter (c1) to improve the fit of the theoretical profile to the experimental profile
• Hydration (water) layer (on by default) - whether to include a hydration layer parameter (c2) to improve the fit of the theoretical profile to the experimental profile
• Experimental background adjustment (off by default) - whether to apply a background adjustment to the experimental profile; this tends to reduce the intensity at high values of q
• Maximal q value (default 0.5) - up to what value of q the profile should be computed
• Profile size (default 500) - number of points in the computed profile
• Implicit hydrogens (on by default) - whether to ignore any explicit hydrogen atoms and consider hydrogen atoms for proteins and nucleic acids implicitly by adding their form factors; for proper recognition of these residues, the structure should have standard PDB atom and residue names. If the structure includes other groups (lipids, sugars, etc.), this option should be turned off and explicit hydrogens added instead.
• Fast coarse-grained profile (off by default)
• Use new plot window (off by default) - whether to show the profile in a new window instead of adding it to the most recent pre-existing plot
• Local executable file (optional) - a local copy of the FoXS executable; if none is specified, the RBVI web service will be used
• Output file location (optional) - local directory in which to place results, stderr, and stdout files

Clicking Calculate Profile computes the theoretical profile and displays it as a solid line. Data points in the experimental profile (if any) are shown as plus signs, and a measure of the quality of fit between the experimental and theoretical profiles, χ, is given in the legend. A lower value of χ indicates a better fit.

Close dismisses the Small-Angle X-Ray Profile dialog. Help opens this manual page in a browser window.

Plots are generated with matplotlib. Icons for manipulating and saving the view are provided below the graph. The mode icons act as toggles: clicking the icon will turn the mode on or off, depending on the current state.

icon	meaning
	default (initial) view
	previous view
	next view
	“pan/zoom” mode (toggle)
	“zoom to rectangle” mode (toggle)
	sliders for graph scaling
	save as image file (it may be necessary to include the proper filename suffix to indicate format: *.png [Portable Network Graphics], *.ps [PostScript], *.eps [Encapsulated PostScript], *.pdf [Portable Document Format], *.svg [Scalable Vector Graphics])