OK, the attached file works. It seems that Modeller is sensitive to the order in which the sequence of the alignment are read.
On 02/04/2015 05:52 PM, Edelmiro Moman wrote: > This is what I get: > > _modeller.ModellerError: chk_aln_340E> Number of residues in model ( > 248) does not match that in alignment ( 221). > > Please, see the attached files. The alignment file and the structure > files work fine with other inputs. > > > On 02/04/2015 05:40 PM, Modeller Caretaker wrote: >> On 2/4/15 8:35 AM, Edelmiro Moman wrote: >>> 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)) >> >> Yes - although you'll need to read the alignment first. There's a method >> read_alignment() which returns it. (Note that this is basically what the >> default loopmodel.select_loop_atoms() method does, except that it >> includes deletions too.) >> >> Ben Webb, Modeller Caretaker > >