Preparing publication-quality molecular figures with PyMOL

About PyMOL and these webpages, further info

The PyMOL GUI

• Getting started with the PyMOL GUI
• Using the command line
• Overview of the protein fold
• Ligand binding

PML scripts

• PML script files: The better way to generate and handle molecular images
• PyMOL selections

Ligands and interactions

• Showing the protein fold and ligand interactions
• Hydrogen bonding interactions
• Large complexes: GPCR & G proteins & peptide ligand (cartoon and surfaces)

Further topics

• Superpositions
• Morphs: visualize a conformational change
• Mapping properties onto a structure - Electrostatic potential, conservation, hydrophobicity/polarity, mobility
• Color AlphaFold predictions by pLDDT
  
• Surfaces: Displaying the electrostatic potential
• Movies: Preparing simple movies to improve spatial perception
• Electron density: Display and analysis of electron density and CryoEM maps
• Installation of PyMOL plugins

Adding labels and composing larger figures using inkscape

• Adding labels and composing larger figures using inkscape