UltraScan Version


SOMO - SAXS/SANS Simulation Options:

Last updated: June 2024

NOTICE: portions of this help file are taken from the Supplementary Materials of "Brookes et al. Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan SOlution MOdeler (US SOMO) enhanced SAS module", J. Appl. Cryst., 46:1823-1833 (2013).

SOMO SAXS/SANS Simulation Options Summary

In this module you can set/change the parameters used by the SAXS/SANS (SAS) and MALS Data Processing and Simulation Module. The module has been split up into several sub-modules, as shown in the above image. The sub-menus can be accessed by clicking on their names.

SOMO SAXS Computation Options

In the SAXS Computation Options: section, the first entry that can be set/changed is the Water electron density (e / A^3): (default: 0.334 e/A3).
Next comes the choice between the computational methods offered: full Debye ("F-DB"), Debye with spherical harmonics ("SH-DB"), a fast methods based on FoXS (Schneidman-Duhovny et al., Nucl. Acids Res. 38, W540-W544, 2010), whose code is only available for Linux operating systems ("quick" Debye, "Q-DB"), and Crysol (Svergun et al., J. Appl. Cryst. 28, 768-773, 1995). If "Q-DB" is selected, it is possible to have at the same time the computation of the P(r) vs. r function by ticking the "P(r)" checkbox. In particular:

Next come a series of entries where various parameters can be set:

In the Quick Debye: Bin size. Smaller bin sizes increase accuracy at the cost of increased computational time. See the FoXS paper reference for details. The default value is that used in the standard FoXS method.

In the Quick Debye: Modulation. The modulation effects the exponential decay of a point scatterer extended from the intensity at q = 0 (I(0)). See the FoXS paper reference for details. The default value is that used in the standard FoXS method.

The next three entries set some Crysol options (the first affects also the SH-DB method):

SH/Crysol: Maximun order of harmonics (default: 15). Increase this number as the size of the structure grows (max for the current Crysol implementation: 40).

Crysol: Order of the Fibonacci grid (default: 17). Increase this number as the size of the structure grows (max for the current Crysol implementation: 18)

Crysol: Contrast of the hydration shell (e/A^3): (default: 0.03 e/A3). Set this parameter to "0" if you want to run Crysol on a structure with explicit hydration waters.

Five checkboxes follow, grouped under Crysol options::

Automatically load difference intensity (default: on). After a Crysol computation, the difference intensity data will be loaded in the graphic window.

Support version 2.6 (default: on).

Support version 3.1+ (default: off).

Shell water (3.1+ only) (default: off). This is a relatively recent new Crysol feature allowing the representation of hydration waters as dummy beads placed on the bio-macromolecule's exterior surface, and their inclusion in the I(q) calculations (see Franke et al., J. Appl. Cryst. 50:1212-1225, 2017).

Crysol: Explicit hydrogens (default: off). By default, Crysol uses implicit hydrogens considered as part of the bound atom and explicit hydrogens are removed. If you wish to use explicit hydrogens specificed in your pdb, then select this option.

SOMO SANS Computation Options

In the SANS Options: section, several parameters can be controlled:

The actual scattering length b at the set D2O fraction Y, b(Y), for each atom i, b(Y)i, is then computed by the program using this equation:

b(Y)i = b(0)i + n(HExch)i * Y * [b(D) - b(H)] * [ 1- f(NHExch)i]

where b(0)i are the neutron scattering lengths of the non-H atoms at Y = 0 and n(HExch)i are the number of exchangeable H attached to them (both tabulated in the hybridization table), b(D) and b(H) are the D and H scattering lengths, respectively, and f(NHNExch)i is the fraction of non-exchanged peptide bond H (which is 0 for all atoms except for the peptide bond N atom), all as defined in this panel (see above). The perdeuteration field is used by Cryson (see below).

As for the SAXS Computation options panel, we have listed a series of alternative methods for the computation of the SANS I(q) vs. q curves. However, only Cryson (Svergun et al., Proc. Natl. Acad. Sci. USA, 95, 2267-2272, 1998) is presently (as of June 2024) active.

The maximum number of harmonics and the order of the Fibonacci grid can be set in the corresponding fields for Cryson. Regarding the Cryson: contrast of the hydration shell field, it is automatically computed from the D2O fraction (see Cryson manual), but the value proposed can be overridden by checking the checkbox provided and entering a different value.

SOMO SAS Curve generation options

The SAS Curve Generation Options: section contains fields whose values are used in the simulation of either a SAXS or a SANS curve.
Enter either the X-ray or neutron wavelength in the Wavelength (Angstrom): field (default: 1.5 A for SAXS; for SANS, an usual value is 6 A).
The span and point density of the simulated curve can be controlled by entering appropriate values in the Starting Angle, Ending Angle, and Angle Stepsize fields, or in the corresponding Starting q, Ending q, and q Stepsize fields, where the transformation from angle units to scattering vector q units is automatically carried over by the program. Default values are 0.001 to 0.6 A-1 q range with a 0.015 stepsize, corresponding to an angular range of 0.014 to 8.214 degrees with a 0.2 degrees stepsize for a wavelength of 1.5 A.

The Normalize P(r) vs r curve by molecular weight is selected by default. Deselecting it will cause the P(r) vs. r curves to be normalized only by their areas.

SOMO SAS bead models options

This module allows selecting the computation of the SAXS and/or SANS coefficients when generating bead models from atomic scale structures (Compute SAXS coefficients for bead models and Compute SANS coefficients for bead models checkboxes), and to optionally use the Rayleigh (Rayleigh, Proc. Royal Soc. London A84:25-46, 1911) structure factors for spheres of uniform electron density (Use Rayleigh (1911) for structure factors checkbox). This procedure is still under development, and will be fully described elsewhere.

The Dummy atom PDB's in NM checkbox is used when uploading bead models whose scale units are not in Å but in nm, like some DAMMIN/DAMMIF-generated models.

SOMO SAS Guinier options

In the SAS Guinier Options menu, the options controlling the Guinier analysis of SAS data can be set, and the various operational modes can be then launched. After setting/revising the options and the parameters, three different Guinier analyses can be launched by pressing "Process Guinier" (conventional Guinier, ln[I(q)] vs. q2), "Process CS Guinier" (cross-section Guinier for rod-like particles, ln[q I(q)] vs. q2), or "Process TV Guinier" (transverse Guinier for disk-like particles, ln[q2 I(q)] vs. q2), respectively.

The general Guinier options that can be set/modified are:

These three controls are active when the "Limit maximum q to maximum q*Rg, q*Rc or q*Rt (not active in Search mode)" checkbox is selected (see below).

The specific Guinier, CS Guinier and TV-Guinier options that can be set/modified are:

The MW and M/L computation options section deals with the parameters that are necessary to perform a correct calculation of <M>w or <M/L>w/z or <M/A>w/z.

Note: from the July 2024 release, the calculations necessary to put the experimental data on an absolute scale can be done directly in the HPLC/KIN module, generating what we have called "I#(q)" and "I*(q)" datasets/files. These files will be automatically recognized and no further calculations will be performed on them, except using an entered concentration for the "I#(q)" datasets.

Otherwise, the conversion from the corresponding experimental <Iexp(0)>w value is done by first putting the data on an absolute scale by normalizing for the intensity extrapolated to 0 scattering angle of a known standard, I(0)std expt for SAXS, according to:

Normalization for SAXS

Then the reduced I(0)* for SAXS in g mol-1 are obtained as:

I(0)* calculation for SAXS

where NA is Avogadro's number, c is the sample concentration [mg ml-1], Re is the diffusion length of the electron [cm], mn is the nucleon mass [g] (note: from 2019, this value by default is taken as 1/NA), vbar symbol is the partial specific volume of the particle [cm3 g-1], ρe is the solvent electron density [e/cm3], and Z and A are the number of electrons and of nucleons, respectively, in the particle, whose ratio is usually taken as a constant specific for each class of biomacromolecules.

If a series of I(q) SAXS curves have been uploaded in the SAS module (for instance, from the HPLC/KIN module), it is possible to set/modify their associated parameters by pressing the Set Curve Concentration, PSV, I0 standard experimental button (see here). As stated above, for already fully pre-processed I*(q) datasets, proper values for these parameters were already employed, and will just be shown by accessing this module. The same partially holds for I#(q) datasets, for which a c value can instead be entered.

When no parameters are entered via the Set Curve Concentration, PSV, I0 standard experimental module, the program will utilize the values as set in this section of the Guinier Options module, which also contains the other parameters necessary for the computation of the <M>w or <M/L>w/z or <M/A>w/z values. In particular:

After properly setting all options/parameters, the computations of the three different Guinier data analysis processes can be launched by pressing either the Process Guinier, or the Process CS Guinier, or the Process TV Guinier buttons.

SOMO SAS Miscellaneous options

In the SAS Miscellaneous Options menu, several controls and limits can be set.

In order to properly compute the I(q) vs. q and P(r) vs. r curves, the SAS module utilizes the atom definition (default: somo.atom), hybridization (default: somo.hybrid) and SAXS coefficients (default: somo.saxs_atoms) tables.
Different tables can be selected by pressing the Load Atom Definition File, Load Hybridization File, and Load SAXS Coefficients File buttons. See the main help for further explanations on the content and use of these tables.

Next come a series of checkboxes:

The Excluded volume WAT [A^3] field allows entering a volume for the SAS hydration water different from the one utilized for the hydrodynamic computations (see the US-SOMO Miscellaneous Options help page). If the field is left blank, the hydrodynamic hydration water volume will be used.

The Excluded volume scaling field allows to modify by a % value the excluded volumes of the non-water atomic groups as tabulated in the atom definition table.

Pressing the Clear remembered molecular weights button will erase stored MW from the program's memory.

A different q range can be entered in the I(q) curve q range for scaling, NNLS and best fit (Angstrom) two fields.

Two new checkboxes where added starting from the March 2023 release:

www contact: Emre Brookes

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Last modified on June 25, 2024.