SASRES manual

Post all your questions about SASRES to the ATSAS Forum.

© ATSAS Team, 2016-2022

Table of Contents

• Manual
  • Introduction
  • Running Sasres
    • Command-Line Arguments and Options
    • Runtime Output
  • Sasres Input Files
  • Sasres Ouput Files
• Examples
  • Command-line execution

Manual

The following sections shortly describe the SASRES approach to asses resolution of ab initio model ensembles, how to run SASRES from the command-line on any of the supported platforms, describe the the required input files and parameters as well as the produced output file.

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

Anne T. Tuukkanen, Gerard J. Kleywegt and Dmitri I. Svergun(2016) Resolution of ab initio shapes determined from small-angle scattering IUCrJ. 3, 440-447.

Introduction

SASRES is a tool to assess the quality and resolution of ab initio shapes reconstructed using small-angle scattering (SAS) data. The Fourier Shell Correlation (FSC) based approach was developed to evaluate the resolution of an ab initio reconstruction using a pre-aligned ensemble of models. Here, the variability of multiple SAS models derived from a single scattering dataset is utilized to estimate the model resolution. It was shown that the average FSC function over an ensemble that reflects the variability of models is directly related to the resolution of the individual models in the shape reconstruction.

Input models are expected to be pre-aligned, either by DAMAVER or possibly CIFSUP, both part of ATSAS, or any other third party application capable of superposition of models. The FSC is calculated pairwise between all the input models provided and the final FSC is calculated as the mean of all pairwise, together with the standard error of the mean. The resolution threshold is at FSC=0.5.

Running Sasres

Usage:

$ sasres [OPTIONS] <FILE(S)>

Here, the FILE(S) argument is a list of ab initio dummy atom or dummy residue models in PDB or mmCIF format.

SASRES does not provide an interactive mode but is completely configurable through its command line options. The ARGUMENTS and OPTIONS known by SASRES are described in the next section below.

Command-Line Arguments and Options

SASRES requires the following command line arguments:

SASRES recognizes the following command-line options.

Runtime Output

There is no runtime output unless the FSC is written to stdout, as per default.

Sasres Input Files

SASRES requires at least an ensemble of three ab initio models as an input.

Sasres Output Files

SASRES computes the average FSC function and estimates the ensemble resolution. The results are written to stdout, or the file name specified with the output option.