Using Rosetta

Rosetta is a computational biology software suite that is used to model macromolecular structures. It has a wide variety of applications such as:

• De Novo Protein Design
• Enzyme Design
• Ligand Docking
• Molecular Structure Prediction

More information on the use cases of Rosetta can be found via their documentation here

Loading Rosetta on Hopper

module load gnu9

module load rosetta

Note that Rosetta does not have any innate visualization tools. To view the output of any Rosetta process like a .pdb file, you must use software like PyMol or ChimeraX.

Using PyRosetta

PyRosetta is an interactive Rosetta-based interface for Python that can be used via Python or Jupyter Notebooks.

To use PyRosetta, you must first install it. Through the cluster, open up a Python environment or Jupyter Notebook (it is recommended that you use a Jupyter Notebook). Then type:

!pip install pyrosetta-installer

import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()

Then, whenever you need to use PyRosetta, open up a Jupyter Notebook or Python environment and type:

import pyrosetta

pyrosetta.init()

Then you should be able to use the PyRosetta functions interactively. Tutorials and documentation on PyRosetta can be found here