Re: [modeller_usage] Automatically find gaps in the alignment

[Edelmiro Moman <>]

Great!

But can I insert that directly within the selection like this?

class MyModel(automodel):
    def select_atoms(self):
        return selection(self.get_insertions(aln, minlength=1, 
maxlength=30, extension=0, include_termini=True))


On 02/04/2015 05:21 PM, Modeller Caretaker wrote:
> On 2/4/15 7:35 AM, Edelmiro Moman wrote:
> > The question is: can Modeller identify and/or report those gaps
> > (position and length) in order to help us to automatise the task?
>
> Of course! See model.get_insertions()
> http://salilab.org/modeller/9.14/manual/node174.html
>
> Given an alignment object, you can also step through its 'positions'
> member:
> http://salilab.org/modeller/9.14/manual/node290.html
>
> Insertions relative to a given sequence are simply those where
> aln.positions[x].get_residue(seq) returns None (i.e. sequence seq has a
> gap at position x).
>
>      Ben Webb, Modeller Caretaker


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Edelmiro Moman, PhD
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