Modelling covalent linkages in CCP4. Issue 6 (24th May 2021)

• Record Type: Journal Article
• Authors: Nicholls, Robert A.; Joosten, Robbie P.; Long, Fei; Wojdyr, Marcin; Lebedev, Andrey; Krissinel, Eugene; Catapano, Lucrezia; Fischer, Marcus; Emsley, Paul; Murshudov, Garib N.
• Is Part Of: Acta crystallographica. Volume 77:Issue 6(2021)
• Page Start: 712
• Page End: 726
• Publication Date: 2021-05-24
• Subjects: covalent linkages -- AceDRG -- CCP4 -- monomer library -- link records -- link dictionary -- mmCIF -- restraints -- CCP4 Monomer Library -- link‐restraint dictionary; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; Molecular biology -- Periodicals; Molecular structure -- Periodicals; Biomolecules -- Structure -- Periodicals; Cytology -- Periodicals; Biomolecules -- Structure; Crystallography; Cytology; Molecular biology; Molecular structure; X-ray crystallography; Periodicals; 548
• DOI: 10.1107/S2059798321001753
• Languages: English
• ISSNs: 2059-7983

Abstract

Abstract : The mechanism for modelling covalent linkages in CCP 4 is reviewed and the method of link‐dictionary generation used by AceDRG is described. An overview of the various protocols available for the modelling and application of covalent linkages within the CCP 4 suite is presented, providing instructive guidelines with a focus on practical application. Abstract : In this contribution, the current protocols for modelling covalent linkages within the CCP 4 suite are considered. The mechanism used for modelling covalent linkages is reviewed: the use of dictionaries for describing changes to stereochemistry as a result of the covalent linkage and the application of link‐annotation records to structural models to ensure the correct treatment of individual instances of covalent linkages. Previously, linkage descriptions were lacking in quality compared with those of contemporary component dictionaries. Consequently, AceDRG has been adapted for the generation of link dictionaries of the same quality as for individual components. The approach adopted by AceDRG for the generation of link dictionaries is outlined, which includes associated modifications to the linked components. A number of tools to facilitate the practical modelling of covalent linkages available within the CCP 4 suite are described, including a new restraint‐dictionary accumulator, the Make Covalent Link tool and AceDRG interface in Coot, the 3D graphical editor JLigand and the mechanisms for dealing with covalent linkages in the CCP 4 i 2 and CCP 4 Cloud environments. These integrated solutions streamline and ease the covalent‐linkage modelling workflow, seamlessly transferring relevant information between programs. Current recommended practice is elucidated by means of instructive practical examples. By summarizing the different approaches to modelling linkages that are available within the CCP 4 suite, limitations and potential pitfalls that may be encountered are highlighted in order to raise awareness, with the intention of improving the quality of future modelled covalent linkages in macromolecular complexes.