Doppio: Relion Single Particle Tutorial
This tutorial shows how to run the Relion Single Particle Analysis pipeline from raw images to fully processed 3D maps using the CCP-EM Doppio GUI.
Doppio: Model Docking and Refinement Tutorial
Using the Doppio GUI this tutorial demostrates how to:
a) fetch and dock an AlphaFold model into a 3D map;
b) refine the model to fit both data and stereochemical restraints automatically using Refmac-Servalcat and manually using Moorhen; and
c) validate the structure with the CCP-EM validation tools.
Buccaneer
Buccaneer is a tool for ab initio model building. The tutorial runs through the procedure for building a new model from a starting sequence, optimising setup parameters and displaying the output model.
Refmac-Servalcat and Coot
Refmac-Servalcat and Coot are tools for automated and interactive model refinement. The tutorial covers map sharpening optimisation, ligand restraint generation (via Acedrug), optimisation of refinement strategy, use of additional restraints, and validation in Refmac followed by model validation and rebuilding in Coot. It was originally used in the 2022 ECM course.
FlexEM
FlexEM flexible fits models into cryoEM density using Modeller.
This tutorial shows how to use the CCP-EM FlexEM interface to fit a homology model of GroEL and was originally used in the 2021 Birkbeck EMBO coure.
Haruspex
Haruspex is a Convolutional Neural Network capable of recognizing and predicting secondary structure elements and nucleotides in Cryo-EM reconstruction density.
This tutorial demostrates shows how to setup CCP-EM to run Haruspex and was originally used in the 2021 SLAC coure.
LocScale
LocScale is a density scaling (sharpening) procedure that aims to enhance the interpretability of cryo-EM density maps.
This tutorial demostrates the use of LocScale to improve map interpretability and was originally used in the 2021 Birkbeck EMBO course
LAFTER
LAFTER is an algorithm for de-noising single particle reconstructions from cryo-EM.
This tutorial shows how to use the LAFTER task in CCP-EM to increase map interpretability and was originally used in the 2021 IUCr Satellite workshop.
Model Validation
Model validation is a task in CCP-EM to assess map and model quality using a variety of global and local metrics. Outlier cluster analysis is performed to highlight regions of structure which require manual inspection/improvement.
This tutorial shows how run this task and was first used in the 2021 IUCr Satellite workshop.
