Shape2SAS¶
Description¶
This tool allows the user to build particles from a series of predefined shapes. By allowing particles to be placed in any location, or orientation relative to an origin, many unique structures can be constructed. Once a structure is created, the user can generate a theoretical data set that can be analysed, or an empirical fitting model can be generated to compare the structure to real data.
Note
The particles are constructed from a series of randomly distributed points within the defined shape. Because of this randomness, creating the same particle two different times may result in subtle differences between scattering curves and slight differences in the resulting empirical models.
The base shapes available to the user include spheres, cylinders, ellipsoids, elliptical cylinders, disks, cubes, cuboids, hollow spheres, hollow cubes, and cylindrical rings. Each of the particles can be individually modified in all dimensions, can be moved to any point in space, and rotated about any point in space. The scattering length density, relative to the medium the particle is in, can also be defined. If the particle is in air, this should be the scattering length density of the particle material.
Using the Tool¶
When the tool is first selected from the menu option, the ‘Build Model’ tab will open. The user can select a shape and ‘Add’ it to the table in the center of the window. The first row of the table is the particle shape, the second row is the scattering length density relative to the solvent, the next three rows are particle dimensions which vary between shapes, the sixth through eighth rows are to position the particle in space, the ninth through eleventh rows define the center of rotation, the 12th through 15th rows define the angles of rotation about the center of rotation and the last row defines the particle color.
The rotation of particles requires further discussion. As mentioned, each particle can be rotated separately from all other particles, but the center of rotation does not need to be the center of the particle, or within the particle volume at all. The RP values define the center of particle rotation. When the alpha, beta, and gamma angles are changed, the individual particle is rotated about the center of rotation. If the center of rotation is the particle centroid, this will result in a rotation with no translation. If the center or rotation is outside the particle, both a rotation and translation of the particle will occur.
Once a series of shapes is defined, the 3D rendering and predicted SAS scattering can be calculated by clicking Plot. The ‘Include Scattering’ checkbox must be selected for the SAS data calculation. If the resulting image does not look as expected, modify the shape table and rerun the calculation until everything is as desired. If two particles overlap in space, by default, the SLD for the particle first generated will be used in the calculation and any subsequent particles in that same volume will be ignored. If the ‘Exclude overlap’ option is unselected, the average SLD within the overlap volume will be calculated and used for the scattering calculations.
Parameter list for each shape particle:
Row |
Parameter |
Description |
|---|---|---|
1 |
Particle name |
The shape selected from the predefined shapes in the combobox. |
2 |
ΔSLD |
The SLD of the particle relative to the medium surrounding it. Defaults to 1.0 |
3, 4, 5 |
Size Definitions |
The sizes for each major axis of the particle, in Å. The inputs will vary based on the shape. |
6, 7, 8 |
COMX, COMY, COMZ |
The particle centroid relative to the coordinate origin, in Å. |
9, 10, 11 |
RPX, RPY, RPZ |
The center of rotation, in cartesian space, about which this particle will rotate, in Å. |
12, 13, 14 |
α, β, γ |
The rotation angle from the point of rotation, about each axis, in degrees. |
15 |
Color |
The color of the points displayed in the particle viewer window. Red, Green, or Blue. |
Once the particle is of the expected form, a few more options are available. The first is the option to generate an empirical model based on the scattering pattern using the ‘To plugin model’ button. This will open a window where you you can select the parameters included in the model and then generate the model. The second option is to run a ‘Virtual SAXS Experiment’ in the second tab of the window. In the second tab, set the Q range, the number of Q points, the number of P(r) points, the number of simulated points within the 3D volume, and any structure factor contributions that may arise. The resulting theoretical curve can be sent to the data explorer where the data set may be treated as any other data set loaded from a file.
References¶
This tool has been adapted from the tool available at https://somo.chem.utk.edu/shape2sas/. For more information on the theoretical basis and calculations performed, please see the paper by Larsen, et. al. https://scripts.iucr.org/cgi-bin/paper?jl5064.
Note
This help document was last changed by Jeff Krzywon, 23May2025