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"# Protein Design with a Resfile and FastRelax\n",
"\n",
"Keywords: FastDesign, FastRelax, ResfileCommandOperation, Resfile, ResidueSelector, MoveMapFactory, TaskFactory, TaskOperation, NoRepackDisulfides, IncludeCurrent, ReadResfile, conf2pdb_chain(), pose_from_rcsb(), create_score_function(), CA_rmsd()"
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"## Overview\n",
"\n",
"In this Workshop, we will learn the classic way to design proteins, but in the same breath introduce the concept of design using a flexible backbone protocol. \n",
"\n",
"This protocol, is essentially design during FastRelax. A separate class, FastDesign, has a bit more options for design, but essentially, they are the same. \n",
"\n",
"Many modern designs have used this FastDesign/RelaxedDesign protocol - including many Science papers from the Baker lab and the RosettaAntibodyDesign (RAbD) protocol that we will cover in another tutorial. \n",
"\n",
"Before this workshop, you should read about the resfile syntax here: https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles"
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"*Warning*: This notebook uses `pyrosetta.distributed.viewer` code, which runs in `jupyter notebook` and might not run if you're using `jupyterlab`."
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"!pip install pyrosettacolabsetup\n",
"import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()\n",
"import pyrosetta; pyrosetta.init()\n"
]
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"**Make sure you are in the directory with the pdb files:**\n",
"\n",
"`cd google_drive/MyDrive/student-notebooks/`"
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