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

[Shawna Frazier <sfrazier@caltech.edu>]

Hi,

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?

Thanks.