#!/usr/bin/env python
# coding: utf-8

# # Structure Refinement

# One of the most basic operations in protein structure and design algorithms is manipulation of the protein conformation. In Rosetta, these manipulations are organized into movers. A `Mover` object simply changes the conformation of a given pose. It can be simple, like a single φ or ψ angle change, or complex, like an entire refinement protocol.
# 
# ## Suggested Reading
# - P. Bradley, K. M. S. Misura & D. Baker, “Toward high-resolution de novo structure prediction for small proteins,” Science 309, 1868-1871 (2005), including Supplementary Material.
# - Z. Li & H. A. Scheraga, “Monte Carlo-minimization approach to the multiple-minima problem in protein folding,” Proc. Natl. Acad. Sci. USA 84, 6611-6615 (1987).
# 
# ## PyRosetta Workshop 5 Link
# https://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta4_online_format/PyRosetta4_Workshop5_StructureRefinement.pdf
# 
# ## Appendix A Link
# https://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta4_online_format/PyRosetta4_Workshops_Appendix_A.pdf

# In[ ]:





# **Chapter contributors:**
# 
# - Kathy Le (Johns Hopkins University); this chapter was adapted from the [PyRosetta book](https://www.amazon.com/PyRosetta-Interactive-Platform-Structure-Prediction-ebook/dp/B01N21DRY8) (J. J. Gray, S. Chaudhury, S. Lyskov, J. Labonte).