There are several mechanisms available in BUSTER to deal with covalent linkages - and it is likely that newer/better methods will come along at some point as well (this is not yet a done and dusted topic, unfortunately):
- Fully automatic (should work for a large number of "standard" cases):
refine ... Pdb2Tnt_RunAdjustLNNN=yes ...
- or -
aB_autorefine ... Pdb2Tnt_RunAdjustLNNN=yes ...
- This relies on LINK records in the input PDB file and is based purely on atom types of the linked atom and all surrounding (i.e. directly bonded) atoms, therefore defining each atom in such a LINK via an atom-type category. For any linkage not yet recognised (as a standard connection by MakeLINK), these "atom-type linkage fingerprints" (ALFs) are used to look up a pre-defined set of linkage restraints - typically bond and angle, but also sometimes torsion and plane restraints - from a distributed database of atom-type categories and resulting linkages $BDG_home/database/files/MakeTNT/adjust_LNNN.db.
- Manual generation of a detailed linkage geometry definition (enables fine-tuning of the resulting description before using it in subsequent refinements) - also for general covalent linkages, not just ligands:
aB_covalent_ligand -h
- To use the newer Grade2 path instead of the default/original one based on the older Grade, set autoBUSTER_CovalentLigand_GradeVersion=2 as a command-line argument.
- For completeness, the original procedure is described here.