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Re: [modeller_usage] Automatically find gaps in the alignment

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






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Edelmiro Moman, PhD
ProSciens, computer-aided drug design
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Attachment: refine_gaps_only.py
Description: application/chimera