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?