A set of scripts in Python and bash to analyse SAXS curves and extract binding patterns

Overall Procedure for SAXScreen

Terminology:

• Raw I(q)-file is the 1d curve directly output from the synchrotron software.
• Buffer-subtracted I(q) is the initial processed one after correction for combinations between sample and ligand buffer.
• Smoothed I(q) is further processed in ATSAS.

Requirements:

• Recent Python with scipy and numpy. On EMBL machines, install a python virtal-environment and use it with this program.

You need to sort and figure out four things:

• List of titration curves and their identities (titration_dictionary)

  • This file contains four columns
  • The name of the titration series (e.g. name of the ligand) to identify and track all data.
  • The sample-ligand ratio indicating the titration point.
  • The volume-wise fraction of ligand aliquot added to the sample during measuement (e.g. 20uL+20uL = 0.5 volume fraction)
  • The location of the raw I(q) file corresponding to this titration point.

• List of ligand curves and their identities (ligand_dictionary)

  • This file contains two columns. The name of the titration series linked to the ligand SAXS-curves

• List of Sample buffer (sample_buffer_list)

  • This file is a simple list of buffer SAXS curves.

• List of Ligand buffer (ligand_buffer_list)

  • This file is a simple list of buffer SAXS curves.

Examine the example files for a better sense of what each file is meant to contain. We will be calling these dictionary files. The script step0-make-simple-saxs-filelist.bash is here to help automatically generate the file listing based on the given title/code of the synchrotron output data.

The only file to copy over are general-settings.txt, and optionally all the step*.bash scripts.

• general-settings.txt attempts to keep all the variable that you're expected to modify in a single place.
• bash scripts are the top-level interface to shell scripts and python commands.