[modeller_usage] R: modelling discarding part of a template

[Anna Marabotti <>]

Right! I knew that there was a simple trick to do it without modifying the
PDB file, but I couldn't remember it...
Thank you very much and best regards
Anna

-----Messaggio originale-----
Da: Modeller Caretaker [">mailto:] 
Inviato: mercoledì 5 maggio 2010 16.55
A: Anna Marabotti
Cc: 
Oggetto: Re: [modeller_usage] modelling discarding part of a template

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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