REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use

A A Vagin; R A Steiner; A A Lebedev; L Potterton; S McNicholas; F Long; G N Murshudov

doi:10.1107/S0907444904023510

REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use

A A Vagin, R A Steiner, A A Lebedev, L Potterton, S McNicholas, F Long, G N Murshudov

Chemistry

Research output: Contribution to journal › Article › peer-review

Abstract

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 REFMAC5. 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 REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.

Original language	English
Pages (from-to)	2184-2195
Number of pages	12
Journal	Acta crystallographica section d-Biological crystallography
Volume	60
DOIs	https://doi.org/10.1107/S0907444904023510
Publication status	Published - Dec 2004

Keywords

CRYSTALLOGRAPHIC INFORMATION FILE
PROTEIN DATA-BANK
MACROMOLECULAR STRUCTURES
REFINEMENT PROCEDURE
COMPUTER-PROGRAMS
ENERGY
MINIMIZATION
MOLECULES
DYNAMICS
SYSTEM

Access to Document

10.1107/S0907444904023510

Cite this

@article{bfec137fbd4a4e9782311cd1a67e8712,

title = "REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use",

abstract = "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 REFMAC5. 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 REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.",

keywords = "CRYSTALLOGRAPHIC INFORMATION FILE, PROTEIN DATA-BANK, MACROMOLECULAR STRUCTURES, REFINEMENT PROCEDURE, COMPUTER-PROGRAMS, ENERGY, MINIMIZATION, MOLECULES, DYNAMICS, SYSTEM",

author = "Vagin, {A A} and Steiner, {R A} and Lebedev, {A A} and L Potterton and S McNicholas and F Long and Murshudov, {G N}",

year = "2004",

month = dec,

doi = "10.1107/S0907444904023510",

language = "English",

volume = "60",

pages = "2184--2195",

journal = "Acta crystallographica section d-Biological crystallography",

issn = "0907-4449",

publisher = "International Union of Crystallography",

}

TY - JOUR

T1 - REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use

AU - Vagin, A A

AU - Steiner, R A

AU - Lebedev, A A

AU - Potterton, L

AU - McNicholas, S

AU - Long, F

AU - Murshudov, G N

PY - 2004/12

Y1 - 2004/12

N2 - 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 REFMAC5. 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 REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.

AB - 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 REFMAC5. 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 REFMAC5 dictionary allows entirely automatic generation of restraints within REFMAC5 refinement runs.

KW - CRYSTALLOGRAPHIC INFORMATION FILE

KW - PROTEIN DATA-BANK

KW - MACROMOLECULAR STRUCTURES

KW - REFINEMENT PROCEDURE

KW - COMPUTER-PROGRAMS

KW - ENERGY

KW - MINIMIZATION

KW - MOLECULES

KW - DYNAMICS

KW - SYSTEM

U2 - 10.1107/S0907444904023510

DO - 10.1107/S0907444904023510

M3 - Article

SN - 0907-4449

VL - 60

SP - 2184

EP - 2195

JO - Acta crystallographica section d-Biological crystallography

JF - Acta crystallographica section d-Biological crystallography

ER -