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Compares calculated scattering profiles to user supplied scattering profiles. Unlike other SASSIE modules experimental curves do not need to be interpolated before analysis.
The SCT Analyze module is accessible from the Retired section of the main menu.
The purpose of the module is to compare models created using the SCT package (primarily via the SCT Calculate module) to experimental scattering curves. In addition to comparing the theoretical and experimental scattering curves structural properties of the coarse grained sphere models used to construct the former are also calculated.
Users will input a YAML SCT parameter file and the neutron or X-ray experimentally obtained curves. The units of Q used in the input scattering files must also be specified (inverse Angstroms or nanometers).
Each Q point in the experimental curve is matched to the nearest Q point in the theoertical curve.
Input experimental curves should be text files with two (Q and I(Q)) or three (Q, I(Q) and I error) columns.
Output Q units are always inverse Angstroms.
This example compares all models for which curves were calculated in run0/sctcalculate to one neutron and two X-ray experimental scattering curves.
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run name: user defined name of folder that will contain the results. sct_calculate directory within this searched for:
SCT parameter file (YAML): File containing SCT modelling parameters (see below for details)
number of neutron curves: Number of experimental curves from neutron scattering to be compared with the theoretical curves.
neutron experimental curve: File containing neurton experimental curve (repeated lines will appear if multiple curves selected).
number of x-ray curves: Number of experimental curves from X-ray scattering to be compared with the theoretical curves.
units of Q in neutron experiment (inverse angstom or nm): Choose units used for Q in the experimental data - 'a' for inverse angstrom or 'nm' for inverse nm.
xray experimental curve: File containing X-ray experimental curve (repeated lines will appear if multiple curves selected).
units of Q in xray experiment (inverse angstom or nm): Choose units used for Q in the experimental data - 'a' for inverse angstrom or 'nm' for inverse nm.
comparison metric: Choice of metric used to assess curve similarity (R factor or reduced Chi square)
An example SCT parameter file can be downloaded from here
Format of the fields which must be contained in the SCT YAML parameter file:
rg:
fitmin: 0.013
fitmax: 0.028
rfac:
qmin: 0.013
qmax: 0.2
Additional ranges can be included to calculate the cross-sectional radii of gyration using sections titles rxs1 and rxs2.
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The output will indicate the number of curves analyzed and the location of the output data.
Results will be written to a new directory (sct_analyze) within the given "run name". Two files are produced:
runname_expt.sum containing a summary of the Rg and Rxs values for all experimental curves.
runname.sum containing summary data for all of the models/curves compared to all of the experimental curves
An example summary file can be found here. The columns are ordered in the following sections: - Model name (based on the frame number for collections created using SASSIE-web) - Model & curve statistics (Rg, Volume etc). for unhydrated models for comparison to neutron data - Curve comparison statistics for neutron experimental data - Model & curve statistics (Rg, Volume etc). for hydrated models for comparison to X-ray data - Curve comparison statistics for X-ray experimental data