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EMBL Hamburg Biological
Small Angle Scattering
BioSAXS
 

AMBIMETER manual

ambimeter

Post all your questions about AMBIMETER to the ATSAS Forum.

© ATSAS Team, 2012-2015

Table of Contents

Manual

The following sections shortly describe the method implemented in AMBIMETER, how to run AMBIMETER from the command-line on any of the supported platforms and the required input files.

If you use results from AMBIMETER in your publication, please cite:

M.V. Petoukhov and D.I. Svergun (2015) Ambiguity assessment of small-angle scattering curves from monodisperse systems Acta Cryst. D71, 1051-1058.

Introduction

Based on the scattering data (the smooth regularized curve produced by GNOM) the program compares it with a library of normalized scattering profiles from 14,000+ shape topologies, selects shapes corresponding to neighboring curves and provides the ambiguity score.

Running ambimeter

Usage:

$ ambimeter [OPTIONS] <GNOMFILE(S)>

OPTIONS known by AMBIMETER are described in next section, the 'GNOMFILE' argument in the section on input files.

Command-line arguments and options

As command line arguments AMBIMETER accepts the filename of a GNOM/DATGNOM output, possibly with relative or absolute path components.

AMBIMETER recognizes following command-line options:

Short optionLong optionDescription
-r --srg Maximum s*Rg in the data range.
-p --prefix Prefix for output file names.
-f --files Specifies which output files to create.
-v --version Print version information and exit.
-h --help Print a summary of arguments and options and exit.

Runtime output

The number of compatible shape topologies, corresponding ambiguity score and prediction of the uniquenes of ab initio reconstruction are printed to stdout.

ambimeter input files

AMBIMETER uses the regularized curve from a GNOM/DATGNOM output file.

Example

$ ambimeter ly01.out
Number of compatible shape categories .................. : 5
Ambiguity score ........................................ : 0.6990
3D reconstruction is potentially unique

  Last modified: July 18, 2017

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