sct_pdb_analysis - Run the Full SCT Constrained Modelling Pipeline

This script combines the functions of all of the other SCT programs to perform the full sphere modelling pipeline. This involves:

Reading input experimental curves, separated into Neutron and X-ray categories.

1. Calculating Rg and Rxs1 from the data and writing to a file
2. Creating unhydrated sphere models
3. IF we have Neutron data:
   • Calculating theoretical scattering curves
   • Comparing theoretical and experimental curves - R factor or $\chi^{2}$
4. IF we have X-ray data:
   • Creating hydrated sphere model
   • Calculating theoretical scattering curve
   • Comparing theoretical and experimental curves - R factor or $\chi^{2}$
5. Writing Rg, Rxs1 and comparison data to a file

Useage:

Run using the command:

sct_pdb_analysis.py [-h] -i [INPUT_PATH] [-o [OUTPUT_PATH]]
                    -p [PARAMETER_FILE] [-x XRAY [XRAY ...]]
                    [-n NEUTRON [NEUTRON ...]] [-t [TITLE]]
                    [-xu {nm,a}] [-nu {nm,a}] [-ou {nm,a}]
                    [--chi2]

Arguments:

-i [INPUT_PATH], --input_path [INPUT_PATH]
                        Path to the input PDB files
-o [OUTPUT_PATH], --output_path [OUTPUT_PATH]
                        Path in which to save output files
-p [PARAMETER_FILE], --parameter_file [PARAMETER_FILE]
                        Path to a file containing input parameters
-x XRAY [XRAY ...], --xray XRAY [XRAY ...]
                        Paths to files containing experimental x-ray
                        scattering curve
-n NEUTRON [NEUTRON ...], --neutron NEUTRON [NEUTRON ...]
                        Paths to files containing experimental neutron
                        scattering curve
-t [TITLE], --title [TITLE]
                        Title to use for summary output file
-xu {nm,a}, --xray_unit {nm,a}
                        Unit for Q in input x-ray data
-nu {nm,a}, --neutron_unit {nm,a}
                        Unit for Q in input neutron data
-ou {nm,a}, --output_unit {nm,a}
                        Unit for Q in output data
--chi2
                        Chose to use Chi squared rather than R factor

Notes:

Default TITLE = sct_output

Output:

Summary file (named TITLE_expt.sum) of the input experimental curves with the following columns:

Filename        Rg      Rxs1

Summary file (named TITLE.sum) of the model data and comparison with experiment with the following header and columns:

Input PDB path: name_edited_pdbs/
       Neutron                                                 X-ray
                                               neutron_file                                            xray_file
Model  Rg_model  Rg_curve  Rxs1_curve  Volume  Rfactor  scale  Rg_model  Rg_curve  Rxs1_curve  Volume  Rfactor  scale

The Model column contains the name of the input PDB file. The headings Rg_model, Rg_curve, Rxs1_curve and Volume are repeated twice. The first set is for the unhydrated model used for comparison to the neutron data, the second for the hydrated model used for x-ray comparisons. After each are the comparisons for each experimental data file (Rfactor/Chi2 and scale). These headings are repeated for each input experimental curve. The scale factor provided is the I(0) value that can be used to match the I(Q)/I(0) theoretical curve to the experimental data.

In the OUTPUT_PATH two sets of directories are created: xray/{curve,models} neutron/{curve,models}

These contain the sphere models and the theoretical curves.