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Re: [modeller_usage] PDB gap fill

Anna Marabotti wrote:
I tried to use the script shown in Wiki "Missing residue" section to
automatically fill a gap of 12 residues in a file PDB. However, the
application stops with the error message: "No loops detected for
refinement: you must redefine select_loop_atoms". I had a look at the
archive and found that 12 residues is the upper limit for loop
detection and refinement, therefore I don't know why Modeller 9v4
does not work in my case. Does anyone have suggestions?

There is no hard upper limit for loop refinement, but in our experience
we find that the conformational space for loops much longer than 12
residues is too large to get reliable sampling.

loopmodel by default will refine loops that are "not too short, not too long". (You can look in automodel.py for the exact criteria.) Note also that the "loop" is not just your 12-residue insertion, but also a couple of residues either side of it. Modeller will actually quite happily refine a loop of *any* length without error, but since the results are not reliable for long loops, you have to explicitly go in and ask automodel to refine them in this case. You can do this by redefining the select_loop_atoms routine. There are examples for this in the manual.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage