Automated comparative modeling with automodel

The simplest way to build comparative models with MODELLER is to use the automodel class. This automates many of the steps required for simple modeling, and can be customized for more complex tasks. A related class, loopmodel, also allows for refinement of loop regions.

See section A.4 for a flowchart of the comparative modeling procedure, and section A.5 for an overview of the loop modeling algorithm.

This chapter gives an overview of simple applications of the automodel class. For more detailed information, see the comparative modeling class reference, in Chapter 4, or the comments in the Python files themselves, modlib/modeller/automodel/automodel.py and modlib/modeller/automodel/loopmodel.py.