Abstract
Biological macromolecules are polymers and therefore the restraints for macromolecular refinement can be subdivided into two sets: restraints that are applied to atoms that all belong to the same monomer and restraints that are associated with the covalent bonds between monomers. The CCP4 template-restraint library contains three types of data entries defining template restraints: descriptions of monomers and their modifications, both used for intramonomer restraints, and descriptions of links for intermonomer restraints. The library provides generic descriptions of modifications and links for protein, DNA and RNA chains, and for some post-translational modifications including glycosylation. Structure-specific template restraints can be defined in a user's additional restraint library. Here, JLigand, a new CCP4 graphical interface to LibCheck and REFMAC that has been developed to manage the user's library and generate new monomer entries is described, as well as new entries for links and associated modifications.
Highlights
Biological macromolecules are polymers and the restraints for macromolecular refinement can be subdivided into two sets: restraints that are applied to atoms that all belong to the same monomer and restraints that are associated with the covalent bonds between monomers
The CCP4 library of template restraints originates from the library which doi:10.1107/S090744491200251X 431 research papers was developed for the Protein Data Bank (PDB; Bernstein et al, 1977) in order to store descriptions of ligands found in macromolecular structures
JLigand is a new CCP4 program for three-dimensional editing of molecular graphs, the generation of corresponding template restraints and their storage in the additional library file, which can be used for model building and refinement together with the standard restraint library
Summary
In the early days of the CCP4 project (Collaborative Computational Project, Number 4, 1994; Winn et al, 2011), the least-squares minimization program PROLSQ (Hendrickson & Konnert, 1980) was adopted as the main macromolecular refinement tool within the project. The CCP4 library of template restraints (further referred to as the restraint library, and known as the monomer library; Vagin et al, 2004) originates from the library which doi:10.1107/S090744491200251X 431 research papers was developed for the Protein Data Bank (PDB; Bernstein et al, 1977) in order to store descriptions of ligands found in macromolecular structures. Along with descriptions of atoms and bond orders, it stores information about covalent bond lengths and angles, torsion angles and lists of chiral centres and planar groups. Another important feature of the restraint library is that it provides definitions of restraints for linkages between the monomers in polymers. JLigand, a more versatile graphical interface for LibCheck, has been developed
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