SAXScreen

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

Introduction

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.

Step-wise Instructions

0) Prepare files and scripts.

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.

1) Then run the scripts in order. Once every parameter is set, then they should all work OK.

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.