Preparing publication-quality molecular figures with PyMOL

About PyMOL and these webpages, further info

Tutorials using the PyMOL GUI

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

Tutorials using pml script files

• Direct link to pml template file
• PML script files: The better way to generate and handle molecular images
• PyMOL selections
• Protein fold and ligand interactions
• A GPCR in complex with a heterotrimeric G protein and a peptide ligand (cartoon and surfaces)
• Superposition of protein structures
• Preparing a morph to visualize a conformational change

Further topics

• Determination of hydrogen bonding interactions
• Mapping properties onto a structure - Electrostatic potential, conservation, hydrophobicity/polarity, mobility
• AlphaFold predictions
• Displaying the electrostatic potential
• Preparing simple movies to improve spatial perception
• Display and analysis of electron density and CryoEM maps
• Installation of PyMOL plugins

Adding labels and composing larger figures using inkscape