Re: [modeller_usage] Building in missing residues from a known structure

[Modeller Caretaker <>]

On 09/12/2012 01:13 PM, Joshua Adelman wrote:
> I've looked through the mailing list archives and online documentation,
> but I'm having some trouble wrapping my head around the proper way to
> accomplish the following. I have two PDB files of a protein in different
> conformations, where in one of the two PDBs, a short stretch of residues
> are missing, but in the other the complete coordinates in that region
> are known. Both PDBs have different missing residues throughout their
> chain, but I'm only interested at this time in modeling that small
> section that's present in one and not in the other.

This is a very simple case of multiple template modeling, very similar 
to question 1 in the FAQ:
http://salilab.org/modeller/9.11/FAQ.html#1

Simply add a third sequence 'C' to your alignment (the sequence you want 
to model) and align it with both A and B, then use regular automodel 
with knowns=('A', 'B') and sequence='C'.

	Ben Webb, Modeller Caretaker
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