datgnom

• Manual
  • Introduction
  • Running datgnom
    • Command-line arguments and options
    • Runtime output
  • datgnom input files
  • datgnom ouput files
• Examples

Manual

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

Introduction

DATGNOM (formerly known as AUTOGNOM) is a tool for automated estimation of the maximum intramolecular distance $D_{max}$, computation of the distance distribution function $p(r)$ and of the smooth regularized scattering curve, i.e. the Fourier transform of $p(r)$. DATGNOM automatically obtains the $p(r)$ function from an indirect Fourier transform of the scattering profile repeatedly using a regularization procedure implemented in the program GNOM.

The optimum $D_{max}$ is determined from automated comparison of the $p(r)$ functions calculated at different $D_{max}$ values ranging from $2\cdot R_g$ to $4\cdot R_g$ with a step of $0.1\cdot R_g$, where $R_g$ is the expected Radius of Gyration. The calculated $p(r)$ functions and corresponding fits to the experimental data are compared using the perceptual criteria of GNOM, where the smoothness of $p(r)$, absence of systematic deviations in the fit, stability of the solution etc. are merged into a total quality estimate. The behaviour of $p(r)$ near $D_{max}$ is taken into account to ensure that the $p(r)$ function goes smoothly to zero.

Running datgnom

Usage:

$ datgnom <SASDATA> [OPTIONS]

OPTIONS known by DATGNOM are described in next section, the required argument SASDATA in the section on input files.

Command-Line Arguments and Options

DATGNOM requires the following command line arguments:

Argument	Description
SASDATA	Exactly one experimental SAS data (.dat) file.

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

DATGNOM recognizes following command-line options:

Short option	Long option	Description
	--seed <N>	Set the seed for the random number generator.
-r	--rg	Expected radius of gyration; typically from the Guinier approximation.
	--first <N>	first point of the data file to use (default: 1)
	--last <N>	last point of the data file to use (default: $s\cdot R_g\approx 8$)
	--discrp <W>	User-defined weight for the Discrepancy criterion
	--oscill <W>	User-defined weight for the Oscillations criterion
	--stabil <W>	User-defined weight for the Stability criterion
	--sysdev <W>	User-defined weight for the Systematic criterion
	--positv <W>	User-defined weight for the Positivity criterion
	--valcen <W>	User-defined weight for the Center criterion
	--smooth <W>	User-defined weight for the Smoothness criterion
-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.

Runtime Output

DATGNOM does not have any runtime output. If the output option is undefined, the regularised SAS data (.out) data is written to stdout.

datgnom input files

DATGNOM expects background-subtracted experimental SAS data (.dat).

datgnom output files

DATGNOM writes regularised SAS data (.out).

Examples