cleave

A cleave task is used to cleave one or more chains in a system. A cleave task requires a single sites subdirective which contains a list of cleavage site desigations. The format for a cleavage site designation is:

<chain>:<resi1>-<resi2>

<chain> is the chain ID, <resi1> and <resi2> are the residue numbers (including optionally appended insertion codes) of the two residues that form the peptide bond. For example, A:12-15 would create a cleavage between residue 12 and residue 15 in chain A.

When a cleavage occurs, all residues in the parent chain N-terminal to the cleavage site retain their original chain ID, while those residues C-terminal to the cleavage site are assigned the first new available chain ID.

An example of a cleave task is shown in Example 15: Fully Glycosylated, Closed SARS-CoV-2 Omicron BA.2 Variant Spike.