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[modeller_usage] Question about alignment.align()

Hello Modeller Users,

I am trying to take a pseudo-symmetric heterodimeric (AB) structure,
and build homodimer (AA) and (BB) structures. The chains have ~30-50%
identity, nearly the same in length.
The way I am doing this is aligning the AA sequence with the AB
sequence derived from the PDB with alignment.align(); However,
Modeller keeps doing something weird at the ends of the second chain,
placing breaks after the first and before the last residue. Chain A is
3 residues shorter than chain B. Example, with underscores inserted
instead of the actual sequence:

template  ___DLH/SVIEN___VNLED/../..
model     ___DLH/H-IAN___VDL-H/../..

I would expect to have the model be "-HIA" in the beginning and "DLH-"
at the end. This is the alignment that I get from Clustal, and the
alignment that makes sense to me. I've tried setting 'overhang=1',
using a number of different matrices from '$LIB', to no avail. With
other matrices (Gonnet), I get a _horrible_ alignment, like so:


How could it insert a gap into a HETATM chain? Is there a better way
to do this, perhaps aligning only the chains that are changed in the
sequence (align A to B), instead of AA with AB?
Thanks for your help!


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