Hello!
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:
File "<string>", line 1, in ?
File "/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py", line 36, in run
self._runlines(self.lines)
File "/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py", line 153, in _runlines
subrout)
File "/Library/modeller-9v2/modlib/modeller/top_interpreter/__init__.py", line 384, in _run_top_cmd
eval('self.topcmds.' + lowcmd + '()')
File "<string>", line 0, in ?
File "/Library/modeller-9v2/modlib/modeller/top_interpreter/commands.py", line 230, in optimize
optimization_method=ometh)
File "/Library/modeller-9v2/modlib/modeller/top_interpreter/topcmds.py", line 412, in optimize
outs = _modeller.mod_top_optimize(mdl, edat, libs, *args)
ValueError: read_op_662E> Invalid choice LONG for variable OUTPUT: can choose one or more from the following: NO_REPORT REPORT
I've tried to change some settings in the .top file but always appear this error.What can I do?
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?
Thank you!! Laura
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
participants (2)
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Laura Lopez -
Modeller Caretaker