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SCT Calculate

Calculates neutron and X-ray scattering profiles from input structures.

Accessibility

The SCT Calculate module is accessible from the Retired section of the main menu.

Basic Usage

The purpose of the module is to use the SCT package to calculate theoretical scattering curves (via coarse grained sphere models) for each frame of an input trajectory.

Users will input a reference PDB file name, and filenames for accompanying PSF topology and trajectory (in either PDB or DCD format) files. Additionally a YAML SCT parameter file must be provided. Users can choose to produce models straight from the input structure for neutron modelling, with a hydration layer for X-ray modelling or both.

Notes

• A coarse grained grid is used to create sphere models from each conformation taken from the input trajectory.

• Hydration modelling is purely geometric; additional spheres are added to those found in the unhdrated model and then filtered to achieve a realistic volume.

• A PSF file is necessary to transform residue names into those required by SCT.

• Sphere models are output in PDB format for each frame.

• Calculated scattering curves are output as two column text files.

Screen Shots and Description of Input Fields

This example creates calculates theoretical X-ray and neutron scattering curves from each of the 20 frames contained in the input trajectory.

\

• run name: user defined name of folder that will contain the results.

• reference pdb: PDB file with naming information for coordinates that will be extracted

• input filename (dcd or pdb): DCD or PDB file with coordinates that will be extracted from.

• psf topology filename: PSF file used to convert PDB naming information to that required by SCT

• SCT parameter file (YAML): File containing SCT modelling parameters (see below for details)

• neutron, X-ray or both?: Select to calculate models and curves for analysis of neutron, X-ray or both types of experiment

• An example SCT parameter file can be downloaded from here

• Format of the fields which must be contained in the SCT YAML parameter file:

sphere:
    cutoff: 4
    boxside: 5.30
hydrate:
    positions: 27
    cutoff: 11
curve:
    qmax: 0.25
    npoints: 100
    radbins: 400
    smear: True
    wavelength: 6.0
    spread: 0.1
    divergence: 0.016

• sphere: Parameters for creation of coarse grained sphere models
  • cutoff: Number of atoms required in a grid cube to create a corresponding sphere
  • boxside: Size of the sides of the grid cubes
• hydrate:
  • positions: Number of spheres added to create candidate hydration shell
  • cutoff: Number of spheres required in a grid cube after hydration to create a corresponding sphere
• curve:
  • qmax: Maximum Q value in for the calculated scattering curve
  • npoints: Number of points in the calculated scattering curve
  • radbins: Number of bins used in teh histogram of inter-sphere distances (Debye equation adapted to spheres)
  • smear: Is a smearing 'correction' to be incorporated for neutron curves
  • wavelength: Wavelength of beam (used for smearing correction)
  • spread: Beam spead (used for smearing correction)
  • divergence: Beam divergence (used for smearing correction)

Example Output

\

The output will indicate the number of frames, and the diectory in which the output was stored.

Results will be written to a new directory (sct_calc) within the given "run name". The results are separated into folders for different experiment types and beneath that for curves and sphere models. For example, in the figure it is noted that the data were saved files within the current project directory within the chosen "run name" directory, this will result in the following directories:

./run_0/sct_calc/neutron/curves
./run_0/sct_calc/neutron/models

./run_0/sct_calc/xray/curves
./run_0/sct_calc/xray/models

Reference(s) and Citations

SCT Documentation: http://dww100.github.io/sct/

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