WK.01 Refmac and Coot Workshop

 This workshop is for macromolecular crystallographers. We will cover macromolecular refinement and model-building, with a particular emphasis on low resolution refinement and the handling of ligands, demonstrating the latest tool and features in Refmac and Coot.


The participants will have the software pre-installed on their system (academics can download for free), but we can bring a set of CDs/DVDs for those (hopefully few) who do not).


- Bonds and angles etc.

- How to define them (mmCIF files)

- Links and how to define them (including JLigand)

- How to acquire and review restraints for known ligands

- How to generate restraints for novel ligands


Model-building Practicalities:

- Downloading scripts

- User-defined key-bindings

- Working with Refmac output

- Ligand representation and interactions


Refinement at Low Resolution:

- Working with NCS

- Working with Jelly bodies      


Model-building at low resolution:

- Rotamer optimisation

- Ramachandran Refinement

- Finding and fixing bumps (Molprobity tools)




Coot Basics:

So that the students are able to load molecules and MTZ data file to see the maps


Refmac Refinement:

Lecture (jelly-body, twinning, sharpening etc)

Hands on: a standard example, use with CCP4i


Restraints lecture:

What are restraints and how do we change them?

Link restraints

Hands on: generation of restraints from SMILES, generation of restraints from 2D description, generation of link restraints



More advanced Coot usage:

Lecture (low resolution tools)

Hands-on: Keybindings, scripting

Placing ligands,

Finding and fixing bumps (Molprobity tools)



Hands-on: More challenging cases: jelly body refinement, twinning, sharpening



Hands on: JLigand, Coot and Refmac together


Time for user-brought problems



Garib Murshudov, [email protected]

Paul Emsley,http://www.bioch.ox.ac.uk/aspsite/research/brochure/emsley/contact.gif


Presenters: Roberto Steiner (King's College, London), Ronan Keegan (CCP4), Garib Murshudov, Paul Emsley


Workshop fee:

$100 students and postdocs

$140 all others

This fee is separate from the registration fee but must be included with your registration. Fees increase after May 31, 2012.