Merging multiple small angle X-ray (SAXS) profiles

Table of Contents

• Introduction
• Setup
• Merging

Introduction

In this example, saxs_merge is used to join multiple profiles from small angle X-ray (SAXS) experiments.

All steps in the procedure use a command line tool called saxs_merge.py. For full help on this tool, run from a command line:

saxs_merge.py --help

Setup

First, obtain the input files used in this example and put them in the current directory, by typing:

cp -r <imp_example_path>/saxs/merge/* .

(On a Windows machine, use 'xcopy /E' rather than 'cp -r'.) Here, <imp_example_path> is the directory containing the IMP example files. The full path to the files can be determined by running in a Python interpreter 'import IMP.saxs; print IMP.saxs.get_example_path('merge')'.

These input files are two SAXS profiles. Each is a text file containing the SAXS data in three columns, corresponding to q, l and err respectively.

Merging

To do the merge, run from the command line:

saxs_merge.py 25043_01C_S059_0_01.sub=10 25043_01D_S061_0_01.sub=10 --auto --header --remove_noisy --remove_redundant --allfiles --outlevel=normal --stop=merging --aalpha=0.05 --bmean=Generalized --cmodel=normal --dalpha=0.05 --emean=Generalized --npoints=200 --acutoff=0.1 --creference=last --cnpoints=200 --eextrapolate=0 --blimit_fitting=240 --elimit_fitting=240 --blimit_hessian=80 --elimit_hessian=80 -v -v -v

A number of output files are produced. For example, data_merged.txt is a single SAXS profile generated by merging all of the input profiles. summary.txt shows the parameters used to do the merge.

Profiles can also be merged using the SAXS Merge webserver.