Re: [modeller_usage] How to deal with a part of protein sequence that have no alignment with the template

[Modeller Caretaker <modeller-care@ucsf.edu>]

xiazhendong1986 wrote:
...
> As we can see from above, the templates have no sequence from amino 1 to 
> 70 to align with the target protein "sldha", and the modelling result is 
> that the structure of sequence 1-70 is a just a long chain with no fold. 
> So how can I get the structure of sequence 1-70?

Modeller is a package for comparative modeling, so if you don't have a 
template,
it won't be able to generate a reasonable-looking model. You may be able 
to find
another template that aligns reasonably well with that range, for example by
using a more sensitive search for templates such as profile-profile.

If you can't find a template for residues 1-70, you have no option with 
Modeller
except to exclude those residues from your model sequence.

	Ben Webb, Modeller Caretaker
--
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