Example: Generating ligand dictionaries for BUSTER refinement

The following example demonstrates how the behaviour of BUSTER has changed from previous releases and how to generate ligand restraint dictionaries.

This uses PDB entry 3mnq.

3mnq is the structure of the myosin motor domain. As well as protein it contains 3 different ligands, namely AD9, STL and EDO.

With previously released versions of BUSTER, in order to refine this structure, one would simply be required to run:

refine -m 3mnq.mtz -p 3mnq.pdb

BUSTER would automatically use restraint dictionaries that were provided either in the distribution or by the user. In this case, the only ligand for which a dictionary was available would have been EDO. For compounds for which no restraint information could be found, STL and AD9 in this case, BUSTER would automatically generate restraints, based on the 3D coordinates in the pdb file.

However, this approach is less than desirable as it simply restrains the geometry of a compound to the observed state and thus any errors in the input geometry will be propagated. With the release of Grade this feature has been disabled in the current release. Running the above command with the current version of BUSTER will result in failure - BUSTER will thus report that it cannot find restraints for AD9 and STL. We provide restraint dictionaries for a limited number of common compounds, including EDO.

In order to run BUSTER now, restraint dictionaries MUST be provided for all of the compounds present.

Generate restraint dictionaries for the above ligands with the command:

grade_PDB_ligand LIG

where LIG is the residue name of the ligand.

grade will successfully generate a refmac-style CIF restraint dictionary for STL. However notice that it will fail on AD9. The reason for the failure with AD9 (ADP Metavanadate) is due to the metal. Whilst grade makes a lot of effort to generate high quality restraint dictionaries, there are some classes of compound that it is currently unable to deal with, specifically compounds containing metals.

In this case, we are left without a dictionary for AD9. However, the dictionary format that BUSTER reads is the same format used by refmac. Thus any of the dictionaries provided by CCP4 (in the $CLIBD/monomers directory) can be used (as can dictionaries generated by other programs such as PRODRG). IN the case of AD9, a dictionary is available in the CCP4 distribution ($CLIBD/monomers/a/AD9.cif).

Once all of the required restraint dictionaries have been provided, by running grade or taken from the CCP4 distribution, BUSTER can be successfully run with the command:

refine -m 3mnq.mtz -p 3mnq.pdb -l STL.cif -l $CLIBD/monomers/a/AD9.cif