There is a very good set of tutorials available from the Erice 2014 workshop. You can follow one of those or work on your own data/problem if you want. Remember that you have a BUSTER reference card to get help - or search this Wiki (box on the upper left).

In the above section the commands you should type into a terminal are shown in green - as in

ls -ltra

The material here is specifically tuned to the length and setup of this workshop.

A good example of using BUSTER (and associated tools) would be 1PMQ.

1. Setup

Create a fresh directory via

mkdir ~/BUSTER-tutorial

and go there with

cd ~/BUSTER-tutorial

You can get the required data files via

fetch_PDB 1PMQ

or save the following files:

You will also need a restraints dictionary for residue 880 - either from or save the file

2. Running BUSTER

To just compute a map you would use the command (check your BUSTER reference card)

refine -p 1pmq.pdb -m 1pmq.mtz -l 880.grade_PDB_ligand.cif -M MapOnly -d MapOnly | tee MapOnly.lis

and then visualise the results using

cd MapOnly

Alternatively, you could run a full series of BUSTER refinements that are rather typical for getting started with BUSTER on a structure without NCS:

refine -p 1pmq.pdb -m 1pmq.mtz -RB  -l 880.grade_PDB_ligand.cif -d 01 | tee 01.lis
refine -p 01/refine.pdb -m 1pmq.mtz -M TLSbasic  -l 880.grade_PDB_ligand.cif -d 02 | tee 02.lis
refine -p 02/refine.pdb -m 1pmq.mtz -M TLSalternate -TLS -M WaterUpdatePkmaps  -l 880.grade_PDB_ligand.cif -d 03 | tee 03.lis

The above is just an example of BUSTER refinements when starting from a deposited PDB structure. Different starting points (poor initial model, domains missing, low-resolution etc) might need a slightly different approach. See the extensive material on this wiki for some pointers ...

3. Visualisation of results

Again, visualisation would be best done via

cd 03

For details about this tool please see here. You will be presented with a box showing you so-called 'unhappy' atoms: thse are atoms you can work through to see if there is something that needs manual attention.


Also, all other Coot tools can be used to analyse your structure - which would show you a potential issue at residue A45:


After correcting this, you can start a quick BUSTER job using the "BUSTER" button at the top right


After pointig to the correct MTZ file (1pmq.mtz) you can just compute a BUSTER map or do a short refinement:


After those initial steps, any subsequent BUSTER refinement would use commands like

refine -p 03/refine-coot-0.pdb -m 1pmq.mtz -M TLSalternate -TLS -l 880.grade_PDB_ligand.cif -d 04 | tee 04.lis


  • use the latest PDB file from manual adjustment in Coot
  • no automatic water-update (since solvent structure already fairly complete and manual work required to get to the 100% level)
  • output of each subsequent run goes into separate subdirectory and we are saving standard output as well (come up withe some meaningful system - here we're using an increasing 2-digit number)

If you want to work with your own structure:

  • look at BUSTER reference card
  • look at material on this wiki
  • if you have NCS:
    • start with -autoncs_noprune -sim_swap_equiv
    • then switch to -autoncs
  • if using TLS:
    • start with -M TLSbasic
    • then switch to -M TLSalternate -TLS
  • difference Fourier maps are described here