João Rodrigues wrote:
> A reply from a newbie as well :)
>
> If I understood your question correctly you have more or less this
> situation:
>
> TEMPLATE AAAAAAAAAA----------AAAAAAAAA
> SEQUENCE AAAAAAAAAABBBBBBBBBBAAAAAAAAA
>
> If you use the FASTA sequence of your template with its own structure,
> it will build a complete structure with those sections modelled as
> loops. You just need to provide MODELLER with the template structure,
> it's sequence (with gaps in the missing regions), and the sequence of
> the full thing.
Exactly right. There is a worked example in the wiki as well:
http://salilab.org/modeller/wiki/Missing%20residues
Ben Webb, Modeller Caretaker
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