BUSTER Example Applications

This page presents a number of practical examples demonstrating how to use different BUSTER features. Some of them use example data from the PDB; a tool for collecting this data in usable format given a PDB code is available from and described here.

Introductory tutorials

• Student level introductory tutorial refining and model building a Molecular Replacement example using BUSTER and coot (rather old: 2010).
• Tutorials on using BUSTER with coot and buster-report can be found at Erice Workshop on Achieving high quality ligand chemistry in protein X-ray structures (2014)

Similarity Restraints

• automated NCS setup using the -autoncs option, the -autoncs_noprune option and -sim_swap_equiv_plus option.
• Using target restraints. Refinement of low resolution ligand-bound structure with target restraints to a high resolution structure.
• Applying NCS to a high resolution structure , including water molecules in NCS restraints

Detailed restraint setup

• CYS-CYS alternate conformations where one disulfide is bonded and the other broken.
• Forcing a zinc ion site to be tetrahedral, utility distance and angle restraints.
• Refining a protein with all hydrogen atoms modelled
• RNA refinement and restraints to favor canonical puckers

Direct use of weighted Quantum Chemical Energy for ligands in BUSTER refinement

• Introduction to QM method
• Introductory example (benzopyran ligand bound to 2i0g)
• Advanced example (raloxifene bound to 2QXS) including higher-order QM

Using TLS models (introduced in 2009)

• An introduction to using TLS with BUSTER
• Example where TLS improves weak density

Occupancy refinement

• Fitting a ligand with coot and then using occupancy refinement because it clearly fits two ways round
• Refining occupancies using manual Gelly scripts

Miscellaneous

• Correcting for wavelength-dependent scattering factor for MSE
• Using autoBUSTER with models and structure factors downloaded from the PDB
• Sorting out molprobity C-beta deviations
• Specifying column and flag value for test set reflections
• Calculating potentially useful difference Fourier maps

Ligand detection modes

• Strategies depending on prior knowledge

Please address problems, corrections and clarifications to buster-develop@globalphasing.com