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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`.

Subsections

- Simple usage
- More advanced usage
  - Including water molecules, HETATM residues, and hydrogen atoms
  - Changing the default optimization and refinement protocol
  - Getting a very fast and approximate model
  - Building a model from multiple templates
  - Building an all hydrogen model
  - Refining only part of the model
  - Including disulfide bridges
  - Generating new-style PDBx/mmCIF outputs
  - Providing your own restraints file
  - Using your own initial model
  - Adding additional restraints to the defaults
  - Building multi-chain models
  - Residues and chains in multi-chain models
  - Accessing output data after modeling is complete
  - Fully automated alignment and modeling
- Loop optimization
  - Automatic loop refinement after model building
  - Defining loop regions for refinement
  - Refining an existing PDB file