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Re: [modeller_usage] loop refinement



Laura Lopez wrote:
I'm trying to obtain refined models of a loop region from a existing pdb file (a model I built before with modeller). I only want to refine a loop, and I've followed the steps in http://www.salilab.org/modeller/manual/node34.html. But it always appears me this error message:
...
ValueError: read_op_662E> Invalid choice LONG for variable OUTPUT: can choose one or more from the following: NO_REPORT REPORT

It's hard to say for sure what your problem is without seeing your script (also, you say you followed the steps in the manual, which show how to write a Python script, but then you talk about a TOP script).

TOP scripts are deprecated, so one solution to your problem is to write a Python script instead, as in the manual. If you really want to use TOP scripts, you may be running into a bug with INITIAL_MALIGN3D - which can be fixed by applying the patch at http://salilab.org/modeller/wiki/Patches - or you are setting OPTIMIZE_OUTPUT to something other than "NO_REPORT" or "REPORT". Otherwise, I'd have to see your script.

Another question: if in the model I've built and from which I've to refine a loop, I had to make a disulfide bridge in this loop, in the loop refinement I also have to make the disulfide restraint?

Sure, if you want the bridge to be preserved.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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