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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

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.

inline image\

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

Example Output

inline image\

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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