A. X-ray Scattering Calculation

SolX program computes the scattering profile using Debye formula:

`f_{j}(q)` is the form factor of jth atom; `r_{j,k}` is the distance between jth and kth atoms; and `g_{j}(q)` is the dummy atom form factor

B. Coordinate-based pair distance distribution function

Pair distance distribution function (PDDF, P(r)) is also calculated from structural coordinates. P(r) and I(q) are related by Equantion (3):

      `P(r) = frac(1)(4\pi^3)int_0^{\infty}I(q)*r*q*sin(r*q)dq`       -- Eqn (3).   

Since `A_j(q)` is a summation of Gaussians, substitute Eqn (1,2) into Eqn(3), `P(r)` can be written as a summation of a series of Gaussian functions in terms of (`r` and `r_{j,k}`). .

C. Anomalous X-ray Scattering

When the incident X-ray energy is in the vicinity of the atomic X-ray absorption edge, the atomic form factor(`f(q)`) in Eqn (1,2) needs an anomalous dispersion correction :

      `f_j^E(q,E) = f_j^0(q) + f_j^'(E) + i f_j''(E)`       -- Eqn (4).   

`f_j^0(q)` is the normal atomic form factor in Eqn (2) and x-ray energy `E`-independent, but `q`-dependent. `f_j^'` and `f_j''` are real and imaginary correction, both are `E`-dependent, but `q`-independent. In anomalous calculations, `f_j^E(q,E)` will be used in Eqn 1-3, instead of `f_j^0(q)`.

SolX Short Instruction

SolX Menu GUI

1. Click on "File" in the menu bar and select "Read Standard PDB File" to read in a coordinate file.

2. Click on "Parameters" in the menu bar and select "Set Calculation Parameters" to set the q min/max for calculation, solvent, etc.

3. Click on "MoleculeType" in the menu bar and select "Set Molecule Type" and then select the priority order for interpreting atom names in the coordinate files. Currently this has to be done every time a new pdb file is read. An editable library of recognized atom name is listed in the file "SolXAtoms.txt" also in the installation directory. If your coordinates are for a protein, pick choice type #3 as the default 1st choice, and you can select the other types as backups to catch atom names in the pdb file that aren't in the protein list. To get all of the atoms in a coordinate file to be recognized, all of the atom names in the pdb file will have to correspond to one of the atom names in the built-in and "SolXAtoms.txt" list.

4. Click on "Calculations" in the menu bar and select "Single Scattering Calculation". Here you can edit the output file name and add an output file tag.

"Fast X-ray Scattering Calculation" and "Fast PDDF Calculation" are recommended for large molecules(~>50 kDa). They use pair distance histogram algorithm.

5. If you have multiple pdb files that will be calculated with the same "Parameters" and "MoleculeType", you can skip step #1, do steps #2& #3, then under "Calculations" menu, click "Multiple Scattering Calculation" to select those pdb files to automatically calculate one by one.

In addition to X-ray scattering, there are other types of calculations available under this menu, for example PDDF/PDF and anomalous etc. More details on these calcuations in later sections.