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

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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