Re: [modeller_usage] modelling discarding part of a template

[Modeller Caretaker <>]

On 5/5/10 3:57 AM, Anna Marabotti wrote:
> I want to model a protein using two different templates, in particular
> they differ in the position of a loop. My protein is very similar to
> template 1, but should have that loop in the same conformation found in
> template 2. So I'd like to "say" to modeller: please model my protein
> using template 1 as much as possible, but use only template 2 to model
> that loop. Please take in mind that both templates cover the entire
> sequence and show the loop (in different conformations).
> I tried to do this by replacing the residues that I would like to be
> discarded (in correspondence of the loop) in template 1 with gaps in the
> alignment. So for example:
>     target: AAAAAAAAAAAAAAAAA
> template 1: BBBB-------BBBBBB
> template 2: ZZZZZZZZZZZZZZZZZ
> (the part with gaps in template 1 is present in PDB file)
> But Modeller returned me an error saying:
> Sequence difference between alignment and PDB:

You have to either keep the complete template sequence in the PDB file, 
or modify the template PDB to remove the residues you don't want. An 
alignment that achieves what you want without modifying the PDB is:

     target: AAAAAAAAAAA-------AAAAAA
 template 1: BBBB-------BBBBBBBBBBBBB
 template 2: ZZZZZZZZZZZ-------ZZZZZZ

	Ben Webb, Modeller Caretaker
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