• Manual
  • Introduction
  • Running nnlsjoe
    • Command-Line
      • Arguments and Options
    • Graphical Interface
  • nnlsjoe Input Files
  • nnlsjoe Output Files
• Examples
  • NNLSJOE for ensemble selection

Manual

The following sections briefly describe the method implemented in NNLSJOE, how to run NNLSJOE from the command-line and describe the required input and the produced output file.

Introduction

NNLSJOE employs non-negative least squares for the selection of an ensemble of models, whose combined theoretical scattering intensity best describe the experimental SAXS data. NNLSJOE can be run using comma separated value files of intensities and size/statistics generated by FFMAKER. Thus the input models describing a pool of conformations may be derived from eg. RANCH or any other program that provides CIF/PDB format.

Running NNLSJOE

Command-Line

Usage:

$ nnlsjoe [OPTIONS] [DATAFILE]

NNLSJOE accepts absolute as well as relative paths.

The OPTIONS known by NNLSJOE are described in the next section.

Arguments and Options

NNLSJOE requires the following command line arguments:

Absolute as well as relative paths to data files are accepted.

NNLSJOE recognizes the following command-line options. Mandatory arguments to long options are mandatory for short options too.

Graphical Interface

As an alternative to usage from the command-line, NNLSJOE may also be run through the EOM wizard from the ATSAS Application Launcher.

This wizard allows convenient generation and selection of pools, as well as their processing and analysis with either GAJOE or NNLSJOE. See EOM for more details.

NNLSJOE input files

NNLSJOE requires exactly one experimental SAS data (.dat) file.

In addition, at least the intensity and ideally the size, as generated by FFMAKER from the pool of models, should be provided.

NNLSJOE output files

NNLSJOE writes a file describing the fit of the selected intensities to the experimental data, and reports the models selected and statistics to stdout.

Examples

NNLSJOE for ensemble selection

Use NNLSJOE to perform selection from a pool of models:

$ nnlsjoe --intensity intensities.csv --size size_statistics.csv datafile.dat

This command runs NNLsJOE against the file datafile.dat, using the pool of intensities file intensities.csv and size/statistic file size_statistics.csv. All models and repeats are considered and the optimum ensemble size determined.