Coot can make an attempt to build missing linking regions or loops 1. This is an area of Coot that needs to be improved, currently O does it much better. We will have several different loop tools here 2. For now there is Calculate -> Fit Gap or the scripting function:
(fit-gap imol chain-id start-resno stop-resno)
and
(fit-gap imol chain-id start-resno stop-resno sequence)
the second form will also mutate and try to rotamer fit the provided sequence.
Example usage: let's say for molecule number 0 in chain "A"
we have residues up to 56 and then a gap after which we have residues
62 and beyond:
(fit-gap 0 "A" 57 61 "TYPWS")