ambimeter

• Manual
  • Introduction
  • Running ambimeter
    • Command-line arguments and options
    • Runtime output
  • ambimeter input files
• Example

Manual

The following sections briefly describe the method implemented in AMBIMETER, how to run AMBIMETER from the command-line and the required input files.

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 the 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 the following command-line options:

Short option	Long option	Description
-r	--srg=<VALUE>	Maximum \(s \cdot Rg\) in the data range.
-p	--prefix=<PREFIX>	Prefix for output file names.
-f	--files=<ARG>	Specifies which output files to create, one of: none, best, all (default: none)
	--model-format=<FMT>	Format of 3D models, one of: cif, pdb (default: cif)
-v	--version	Print version information and exit.
-h	--help	Print a summary of arguments, options, and exit.

Runtime output

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

ambimeter input files

AMBIMETER requires regularised SAS data (.out) as generated by GNOM.

Example

To calculate the ambiguity score only, run ambimeter as:

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

To obtain the most compatible shape in the default mmCIF format:

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

To obtain all compatible shapes, here 5, in PDB format:

$ ambimeter ly01.out --files=all --model-format=pdb
Number of compatible shape categories .................. : 5
Ambiguity score ........................................ : 0.6990
3D reconstruction is potentially unique