There is not a lot of time for running more complicated BUSTER refinements on large structures during the tutorial. So it might be a good idea to work with something smaller and faster to get a first idea about how to run BUSTER - like the this tutorial.

Working with your own data

This is of course the most interesting part. Remember to have the following available:

  • a PDB file of your current model (including the correct SSBOND and LINK records
  • a MTZ file with amplitudes (F and SIGF, but actual column names don't matter) and a test-set flag (usually named FREE or such)
  • restraint dictionaries for any more unusual ligand/compound
    • either from using our Grade webserver
    • or by using an existing dictionary from $CLIBD/monomers/a/ABC.cif (adapting the residue name accordingly)

Make sure you have your reference card printout handy.

The most basic command could be

refine -p your.pdb -m your.mtz -autoncs -d 01 | tee 01.lis

If you don't have NCS (multiple copies of the same macromolecule in the asymmetric unit), you could leave the -autoncs flag out. But since it won't have an effect in that case it might be a good idea to always use that flag by default.

If you have NCS, but the individual copies might have seen some undesired divergence, using -autoncs_noprune -sim_swap_equiv might be a better idea to re-introduce some of the lost NCS relations. This could be beneficial if e.g. Coot was allowed to fix nomenclature errors upon startup (often resulting in destroying accurate NCS relatoin between related copies of symmetrical side-chain amino-acids), or if during manual model building changes in one chain are not appropriately transfered onto the other chains.

A first BUSTER refinement could always start with a simple rigid-body cycle: just add the -R flag to the first BUSTER job.

If you want to try TLS parametrisation (at later stages of refinement), add -M (and [-M TLSalternate -TLS] for subsequent cycles).

Water addition can be switched on via the -M macro switch.

In case you want to see if a ligand might have bound: use the -L flag for detecting any bound ligand and providing improved difference maps for manual or automatic (via Rhofit) ligand fitting.