Keywords: manual

Next: loopmodel.loop.md_level control Up: loopmodel reference Previous: loopmodel reference Contents Index

## loopmodel() -- prepare to build models with loop refinement

`loopmodel(env, sequence, alnfile=None, knowns=None, inimodel=None, deviation=None, library_schedule=None, csrfile=None, inifile=None, assess_methods=None, loop_assess_methods=None)`

> This creates a new object for loop modeling. It can either build standard comparative models (in identical fashion to the `automodel` class) and then refine each of them, in which case you should set the alnfile and knowns arguments appropriately (see the automodel() documentation) or it can refine a given region of a PDB file, in which case you should set inimodel to the name of the PDB file instead. In both cases, sequence identifies the code of the target sequence.

> All other arguments are the same as those for automodel(), with the exception of those below:

> loop_assess_methods is the analog of automodel.assess_methods for loop modeling, and allows you to request assessment of the generated loop models. (This can also be set after the object is created, by assigning to `'loopmodel.loop.assess_methods'`.)

> See section 2.3 for examples.

Next: loopmodel.loop.md_level control Up: loopmodel reference Previous: loopmodel reference Contents Index