David, if you know well what kind of residues are involved, you  
might be able to do that using "connect" applied to a combination of 
atom IDs and distances.

say,
connect 3.0 (AS?.N??) (SER.O??) hbond
to create Hbonds between nitrogen atoms in Asx and oxygen atoms in 
serine if they are less than 3 angstroms apart

(Just an idea)


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