ligate¶
During a psfgen task, pestifer can be configured to “cap” the ends of interior gaps in protein backbones, or it can model-in the missing residues by growing them in from the C-terminus of the resolved protein before the gap. Ligation refers to forming the bond between the C-terminus of the modeled-in residues and the first resolved residue after the gap. This is done by “steering” the C-terminus toward the first resolved residue after the gap and then patching the bond in using the CHARMMFF LINK patch.
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