Coot download ccp42/11/2023 A number of tools to facilitate the practical modelling of covalent linkages available within the CCP4 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 CCP4 i2 and CCP4 Cloud environments. The approach adopted by AceDRG for the generation of link dictionaries is outlined, which includes associated modifications to the linked components. Consequently, AceDRG has been adapted for the generation of link dictionaries of the same quality as for individual components. Previously, linkage descriptions were lacking in quality compared with those of contemporary component dictionaries. 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. In this contribution, the current protocols for modelling covalent linkages within the CCP4 suite are considered.
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