Remember that you have a BUSTER reference card ({file:buster_referene_card.pdf}) to get help - or search this Wiki (box on the upper left).

In the sections below, the commands you should type into a terminal are shown in green - as in

  ls -ltra

The main command you will be using is the command "refine". This comes with inline help via

  refine -h

which will also point you to the locally installed manual.

You can request a licence for BUSTER (free to academics) at


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

1. Setup

Create a fresh directory e.g. via

  mkdir ~/BUSTER-tutorial

and go there with

  cd ~/BUSTER-tutorial

(or use some other location if you want). You can get the required data files via

  fetch_PDB 1PMQ

(Note: this will not work at the moment as expected, since 1PMQ was superseded by 4Z9L).

This tool can be used to fetch any model/data from the PDB, resulting in two files:


Or save the following files:

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

2. Running BUSTER

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

  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 or when switching from a different refinement program to BUSTER. 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

The results of a BUSTER refinement can be loaded into Coot using e.g.

  cd 03
  coot --pdb refine.pdb --auto refine.mtz

But visualisation might be better 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: these 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 pointing to the correct MTZ file (1pmq.mtz) you can just compute a BUSTER map or do a short refinement:


4. Follow-up refinements

Following 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


Working with your own data

If you want to work with your own structure: