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[modeller_usage] the pdb template has a break in the chain


I am having an issue where the pdb template contains a chain break but the model I produce is not broken.

The pdb template I am using (2bg9.pdb) is already an oligomer with subunit chains denoted by " / ", but each subunit chain is missing a considerable stretch of sequence (the intracellular portion) so each subunit chain is broken into two pieces in the structure. My resulting model structure, however, is not broken.

Is there a way I can add a command to break the bond in my model?