hybrid Small Angle Scattering — hands-on guide

This guide is designed to provide users with practical advice on using the hySAS module. For theoretical information about the method, please refer to the related manuscript. The guide is divided into several sections:

hySAS Intro & Overview

A brief introduction to the method, basic concepts, and an overview of the analyses that can be performed.

Determining the Scattering Profile with hySAS

From coordinates to a SAS curve: steps and examples to analyse a PDB file or a trajectory.

Generating a Conformational Ensemble with GMX and hySAS

Combining GROMACS and PLUMED to generate conformational ensembles restrained by SAS data using different coupling methods.

Preparing the Input Files

Guidelines and tips for preparing the input files.

Compiling PLUMED with ARRAYFIRE Support

Technical suggestions and a real-case example for installing PLUMED with ARRAYFIRE support on a SLURM-based HPC.

flowchart TB
  A[hySAS intro & overview]
  A --> B[Tutorial-1: <br> Determining the scattering profile with hySAS]
  B --> C[Tutorial-2: <br> Generating a conformational ensemble with GMX and hySAS]

  D[Technical Support: <br> Preparing the input files]
  D --> E[Technical Support: <br> Compiling PLUMED with ARRAYFIRE support]
  
  click A "intro.html" "hySAS intro & overview"
  click B "01.html" "Tutorial-1: Determining the scattering profile with hySAS"
  click C "02.html" "Tutorial-2: Generating a conformational ensemble with GMX and hySAS"
  click D "input.html" "Preparing the input files"
  click E "arrayfire.html" "Compiling PLUMED with ARRAYFIRE support"

Click here to open manual pages for actions discussed in this tutorial.