The Proteins are Beautiful in PyMol resources show students how to use the powerful protein structure visualization software PyMOL to observe and analyze structures, to prepare protein files for modeling, and to create clear, intuitive figures for publication. Try your hand at scripting in PyMol to automate your protein structure beautification processes.

3.1.1 Intro to PyMol: Part 1 This slide deck covers: downloading PyMol, loading PDBs with the GUI and with Fetch command, mouse controls/trackpad shortcuts, displaying sequence, selecting and finding residues, recoloring, the PyMol Wiki. Author: Audrey Olshefsky.

3.1.2 Intro to PyMol: Part 2 This slide deck covers the PDB: what it contains and how to navigate, a refresh on some of the topics covered in Part 1, showing sticks, more details on coloring, printing the amino acid sequence, exporting selections, measuring alpha carbon distances, removing residues, viewing multimeric structures. Author: Audrey Olshefsky.

3.1.3 Guide: intro to Navigating PyMol This guide walks students through step-by-step on how to download and basic PyMol navigation.

3.1.4 Guide: Protein Data Bank features and PDB structure file download This guide walks students through step-by-step on how to navigate the Protein Data Bank (PDB), search for structures, use the PDB resources, and download files.

3.2 Making Figures in PyMol This slide deck covers: changing background color, running pymol scripts, exporting images, creating new objects. The last few slides in this deck show examples of pre- and post- PyMol beautification processes. Author: Audrey Olshefsky.

3.3 Guide: PyMol visualization differences between aligned protein structure files This short guide walks students through how to align two structures and how to highlight some of the variations.