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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