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EMBL Hamburg Biological
Small Angle Scattering
BioSAXS
 

DATABSOLUTE manual

databsolute

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© ATSAS Team, 2017

Table of Contents

Manual

The following sections shortly describe how to run DATABSOLUTE from the command-line on any of the supported platforms, the required input and the produced output files.

Introduction

DATABSOLUTE may be used to scale concentration normalized data to absolute scale using water as a standard. The forward scattering of water can be calculated as it only depends on the isothermal compressibility and the temperature. To scale a sample to absolute scale a calibration factor needs to be obtained. Data of the water and the empty capillary is collected, and a subtracted curve is obtained. To obtain the forward scattering of water, the intensity plateu between 0.2-0.5A is averaged. Finally, this forward scattering is divided by the calculated forward scattering, resulting in a calibration factor. It is important that the water used for calibration is measured at the same temperature as the sample intended for absolute scaling.

Running databsolute

Usage:

$ databsolute <FILE> <FILE> <FILE> [-o FILE]

OPTIONS known by DATABSOLUTE are described in next section, the required FILE arguments in the section on input files.

Command-line arguments and options

DATABSOLUTE requires the following command line arguments:

ArgumentDescription
FILE The file containing scattering from the water at the same temperature as the sample.
FILE The file containing the scattering from the empty cell (e.g. empty capillary scattering).
FILE The file containing the sample to absolute scale. Should be normalized by concentration.

Absolute as well as relative paths to data files are accepted. Up to one of the input files may also be given as '-', in this case input is read from stdin instead of a file.

DATABSOLUTE recognizes following command-line options:

Short optionLong optionDescription
--first=<N> First data point to use for finding the experimental forward scattering, default is 100. Data point should be at the plateu.
--last=<N> Last data point to use for finding the experimental forward scattering, default is 1000. Data point should be at the plateu.
--temperature=<T> Temperature of the water used for calibration. If empty, the program checks file containing the water scattering for the temperature. If not found, the default temperature is 20 degrees Celsius.
-o --output=<FILE> Specify a FILE where to write the absolute scaled data to, the FILE may contain relative or absolute path components. By default the result is written to stdout.
-v --version Print version information and exit.
-h --help Print a summary of arguments and options and exit.

databsolute input files

Input files for databsolute may be in any of the supported data formats as long as scattering vector, experimental intensity and errors are available. The scattering of the water should ideally be measured at the same temperature as the sample intended for absolute scaling. The scattering of the water and the empty cell should be on the same grid to allow subtraction.

databsolute output files

The produced output file contains the data on an absolute scale. It also contains the file name of the water and empty cell scattering used, as well as the temperature and the calibration factor.

Example

$ databsolute water_001.dat cap_002.dat bsa_003.dat -o bsa_absolute_scale.dat

  Last modified: June 26, 2017

© BioSAXS group 2017