Re: [modeller_usage] Homology modeling with low sequence identity and missing loops in template

[Modeller Caretaker <>]

On 9/2/19 4:00 PM, Ahmad Khalifa wrote:
> I have two sequences with low sequence identity and I get an alignment 
> in modeller different than clustalW, which also differs from when I use 
> emboss matcher.

This is unsurprising, since different algorithms are likely being used 
here to make these alignments.

> I also have a missing segment in my template, I want the final model to 
> have the corresponding segments and the gaps unmodeled, same as the 
> template.

If you don't want part of the sequence in the model, exclude it from 
your alignment. Modeller only models the sequence you give it. You may 
need to add a chain break (/ character) to the alignment to prevent 
Modeller from trying to connect the residues on either side of the gap 
with a peptide bond.

	Ben Webb, Modeller Caretaker
--
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