# More advanced usage

Subsections

- 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