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SCT

A suite of tools for atomistic modelling of SAS data

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sct - Calculate Scattering Curve from a Sphere Model

Create a theoretical scattering curve (I/I(0) vs $Q$) from a sphere model using the Debye equation. Units of $Q$ are Angstrom$^{-1}$. For theoretical neutron curves smearing can be added as described in S. J. Perkins & H. Weiss, (1983) J. Mol. Biol. 168, 847-866

Useage:

Run using the command:

sct

This will produce the following prompts, you should provide the inputs shown in italics. Individual values to input are surrounded by square braces. When multiple values are requires they can either be separated by a space on the same line or entered on separate lines. The meaning of the input values are explained in the Notes section.

Enter name of file containing model coords [sphere model]

Enter name of file for the calc curve [curve file]

Enter name of file containing more info [output file]

TITLE ? [title]

DEFAULT PARAMETERS? Y=1 N=0 [use defaults]

If you answer '0' to the above question you will recieve the following prompts too:

  • PLOTS? Y=1 N=0 [plots]
  • SMEARING? Y=1 N=0 [smearing]
  • If you answer '0' to the smearing question you will recieve the following prompts too:
    • WAVELENGTH SPREAD? 0.13?
    • WAVELENGTH? 5.97?
    • BEAM DIVERGENCE? 0.016? NOT 0 [spread] [wavelength] [divergence]
  • MAXIMUM Q VALUE? [max Q]
  • RADIUS TO BE LOW AND CHECKED RADIUS OF ONE SPHERE? [rr]

Notes:

  • sphere model = input sphere model coordinates in a text file consisting of four columns (column width of 10 characters, 2 decimal places), as generated by brktos. Columns are X, Y, Z coordinates and sphere radius

  • curve file = path to output $I/I_o$ vs $Q$ file

  • output file = path to file which will summary output concerning the curve calculation

  • plots = old parameter used to invoke GUI, no longer available kept for historical compatability

  • smearing = choice of whether to include smearing (for comparison with neutron experimental results)

  • spread = spread of the neutron beam for smearing calculation ($\Delta \lambda / \lambda$)

  • wavelength = wavelength of neutron beam for smearing calculation ($\lambda$)

  • divergence = divergences of neutron beam for smearing calculation

  • max Q = maximum value of Q to claculate the curve up to

  • rr = radius of sphere used in form factor calculation for the Debye equation

Output:

curve file contains two columns $I/I_{0}$ and $Q$. $Q$ is in units of $\AA^{-1}$.