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
- 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)
So that the students are able to load molecules and MTZ data file to see the maps
Lecture (jelly-body, twinning, sharpening etc)
Hands on: a standard example, use with CCP4i
What are restraints and how do we change them?
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
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]
Presenters: Roberto Steiner (King's College, London), Ronan Keegan (CCP4), Garib Murshudov, Paul Emsley
$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.