Shawna Frazier wrote: > I am having an issue where the pdb template contains a chain break but > the model I produce is not broken.
If you want a chain break in your model, you need a chain break "/" in your *model* sequence.
> 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.
You didn't post your alignment, but it sounds like you have something like
template AAAAAA----------AA/BBBBBBBB---------BBBBB* model aaaaaa----------aa/bbbbbbbb---------bbbbb*
It sounds like you want something like
template AAAAAA----------AA/BBBBBBBB---------BBBBB* model aaaaaa/---------aa/bbbbbbbb/--------bbbbb*
Ben Webb, Modeller Caretaker