Open AccessREFMAC 5 dictionary: organization of prior chemical knowledge and guidelines for its use
Author(s) -
Vagin Alexei A.,
Steiner Roberto A.,
Lebedev Andrey A.,
Potterton Liz,
McNicholas Stuart,
Long Fei,
Murshudov Garib N.
Publication year - 2004
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444904023510
Subject(s) - macromolecule , computer science , monomer , nucleic acid , set (abstract data type) , polymer , artificial intelligence , chemistry , organic chemistry , programming language , biochemistry
One of the most important aspects of macromolecular structure refinement is the use of prior chemical knowledge. Bond lengths, bond angles and other chemical properties are used in restrained refinement as subsidiary conditions. This contribution describes the organization and some aspects of the use of the flexible and human/machine‐readable dictionary of prior chemical knowledge used by the maximum‐likelihood macromolecular‐refinement program REFMAC 5. The dictionary stores information about monomers which represent the constitutive building blocks of biological macromolecules (amino acids, nucleic acids and saccharides) and about numerous organic/inorganic compounds commonly found in macromolecular crystallography. It also describes the modifications the building blocks undergo as a result of chemical reactions and the links required for polymer formation. More than 2000 monomer entries, 100 modification entries and 200 link entries are currently available. Algorithms and tools for updating and adding new entries to the dictionary have also been developed and are presented here. In many cases, the REFMAC 5 dictionary allows entirely automatic generation of restraints within REFMAC 5 refinement runs.