[modeller_usage] Re: Modelling based on two templates - one oligomer and one monomer

[Modeller Caretaker <>]

On 3/19/24 8:38 AM, hmad3--- via modeller_usage wrote:
> What if I am modelling with ligands? Would the following be right?
> temp1    AAAA./AAAA/BBBB./BBBB/BBBB*
> temp2    aaaa-/----/----/----/----*
> temp3    ----/-----/bbbb-/----/----*
> model    aaaa./aaaa/bbbb./bbbb/bbbb*

Yes. Normally I would align the chain breaks with each other to make it 
more clear to a human reader, but Modeller doesn't distinguish a chain 
break from a gap in a template.

> (The .pdb files for temp2 and temp3 have no ligands. Should the
> ligand  be indicated? If so, with a "-" or "."?)

The sequence for a template must match what's in the PDB file. So if 
there is no ligand, there should be no ".". Normally you would put a gap 
here so that the target does not align with anything else in that 
template at that position. (Generally it only makes sense for a target 
ligand to align with a single template ligand.)

	Ben Webb, Modeller Caretaker
-- 
             https://salilab.org/modeller/
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