I have encountered a persistent error message when using Modeller for generating initial structures with automatic loop modelling. Please find attached a copy of the alignment file etc
The error message is -
Traceback (most recent call last): File "valid.py", line 25, in ? a.make() # do homology modeling File "/usr/lib/modeller9v1/modlib/modeller/automodel/loopmodel.py", line 31, i n make automodel.make(self, exit_stage) File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 119, in make self.multiple_models(atmsel) File "/usr/lib/modeller9v1/modlib/modeller/automodel/loopmodel.py", line 48, i n multiple_models self.build_seq(filename, num) File "/usr/lib/modeller9v1/modlib/modeller/automodel/loopmodel.py", line 115, in build_seq atmsel = self._check_select_loop_atoms() File "/usr/lib/modeller9v1/modlib/modeller/automodel/loopmodel.py", line 278, in _check_select_loop_atoms atmsel = self.select_loop_atoms() File "/usr/lib/modeller9v1/modlib/modeller/automodel/loopmodel.py", line 315, in select_loop_atoms raise ModellerError, \ _modeller.error: No loops detected for refinement: you must redefine select_loop _atoms
Does this indicate that there are no gaps in the initial model that can be refined, automatically, by loop modelling?
Regards
Mike Paterson
Michael Paterson wrote: > I have encountered a persistent error message when using Modeller for > generating initial structures with automatic loop modelling. Please > find attached a copy of the alignment file etc > > The error message is - ... > _modeller.error: No loops detected for refinement: you must redefine > select_loop _atoms > > > Does this indicate that there are no gaps in the initial model that > can be refined, automatically, by loop modelling?
Exactly. If you want loop refinement of a specific region, you must select that set of residues by redefining the select_loop_atoms routine. There are examples for this in the manual. The "automatic" selection of loops uses a very simple set of criteria: it selects all gaps in the alignment, extending the selection by two residues either side of each gap, and accepting only final loops that are at least 5, but no more than 15, residues long. See the select_loop_atoms Python code in the modlib/modeller/automodel/loopmodel.py file, and also http://salilab.org/modeller/9v2/manual/node168.html
In your case, it looks like you have only one major loop in your model, but it is far too long to be amenable to loop modeling (12 residues is essentially the practical limit).
Ben Webb, Modeller Caretaker
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Michael Paterson -
Modeller Caretaker