databsolute

• Manual
  • Introduction
  • Running databsolute
    • Command-line arguments and options
  • databsolute input files
  • databsolute output files
• Examples

Manual

The following sections briefly describe how to run DATABSOLUTE from the command-line, the required input and the produced output files.

Introduction

DATABSOLUTE facilitates the conversion of concentration-normalized data to an absolute scale, using water as a reference standard.

To scale experimental scattering data to absolute scale, the scattering of water and the empty measurement cell has to be collected in addition to any sample of interest. DATABSOLUTE subtracts the scattering of the empty cell from the water scattering and subsequently calculates the forward scattering of water, which only depends on the isothermal compressibility and its temperature. Hence, the water scattering is assumed to be flat in a certain region of data points, where it is averaged.

Finally, the data to be converted to absolute scale is divided by the calculated forward scattering and multiplied by the isothermal compressibility of water at the given temperature. The resulting data is written to stdout or a specified file.

Running databsolute

Usage:

$ databsolute <WATER> <CELL> <SAMPLE> [-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:

Argument	Description
WATER	Scattering of water at the same temperature as the sample.
CELL	Scattering of the empty sample holder, e.g. a capillary.
SAMPLE	Experimental data to scale to absolute scale, Must previously be normalized by concentration.

Absolute as well as relative paths to all data files are accepted. Instead of a file name, one of the arguments may be given as ‘-‘ to read data from stdin.

DATABSOLUTE recognizes following command-line options:

Short option	Long option	Description
	--first <N>	First data point to use to calculate the experimental forward scattering; default: 100.
	--last <N>	Last data point to use to calculate the experimental forward scattering; default: 1000
	--temperature <T>	Temperature of the water used for calibration. If empty, the program attempts to detemine the water temperature from key-value pairs in the footer of the WATER file. If not found, a default temperature of 20°C is assumed.
-o	--output <FILE>	Relative or absolute path to save the result; if not specified, the result is printed to stdout.
-v	--version	Print version information and exit.
-h	--help	Print a summary of arguments, options, and exit.

databsolute input files

DATABSOLUTE expects experimental SAS data (.dat). The scattering of water should ideally be measured at the same temperature as the sample intended for absolute scaling. All experimental data files should have the same angular spcaing to avoid the necessity of re-grid.

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.

Examples

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