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:
VNLED/../.. VDLH/-../..
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!
Vadim