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