Tutorial

Overview

In this tutorial, we will show how to set up a system for a FFEA simulation, and how to visualise and analyse the resulting trajectory via the FFEA analysis toolkit. For this example, we will be using the GroEL protein chaperone from the RSCP PDB.

A python script packaged with some PDB and EMDB files is available to download here if you want to skip the GroEL mesh generation tutorial and get straight to running a FFEA simulation.

For further details on setting up a simulation, please refer to the next chapter of this manual.

Content:

• Quickstart
• Obtaining an EDM
• EDM to Surface Profile
• Coarsening a Surface Profile
• Surface Profile to Volumetric Mesh
• Volumetric Mesh to FFEA
• Running a Simulation
• Visualising FFEA
• Analysis, and FFEA tools
• Recovering Atomic Resolution
• Using FFEA_rod