Common PyMOL Mistakes and How to Fix Them: Troubleshooting Guide 12 min read All levels Most PyMOL problems have simple causes and two-line fixes — but only if you know where to look. These are the ten issues that appear most often in PyMOL help threads, lab Slack channels, and frustrated emails to supervisors at…
PyMOL vs VMD vs ChimeraX: Which Molecular Visualization Tool Should You Use? 13 min read All levels Three tools dominate molecular visualization in structural biology and computational chemistry. They’re not interchangeable — each is genuinely better than the others for specific tasks. This guide gives you the honest comparison that helps you pick the right…
How to Measure Distances and Angles in PyMOL: Complete Guide 10 min read Beginner to intermediate Every structural biology paper reports distances — H-bond lengths, active site geometries, domain separations. PyMOL makes these measurements trivial once you know the right commands and how to display them cleanly in publication figures. Contents Two ways to measure:…
PyMOL Scripting for Beginners: Automate Repetitive Tasks with Python 13 min read Beginner to intermediate If you’ve typed the same ten PyMOL commands more than twice, you’re ready to script. PyMOL’s scripting environment is Python — which means every Python skill you already have translates directly. This tutorial takes you from your first saved script…
How to Color AlphaFold Structures by pLDDT in PyMOL: Confidence Visualization Guide 11 min read Beginner to intermediate Every AlphaFold structure comes with per-residue confidence scores encoded directly in the PDB file — but only if you know where to look and how to visualize them. This tutorial covers the complete workflow from loading an…
How to Visualize Molecular Dynamics Trajectories in PyMOL: Animation, Key Frames and Export 12 min read Intermediate MD trajectories contain the full dynamic story of how a protein moves — but that story is invisible until it’s visualized. This tutorial covers loading trajectories from GROMACS and AMBER into PyMOL, controlling playback, making smooth animations, capturing…
How to Visualize Protein-Ligand Interactions in PyMOL: Binding Pockets, H-bonds and Publication Figures 13 min read Intermediate Protein-ligand interaction figures are among the most published images in structural biology and drug discovery. This tutorial covers the complete workflow: loading the complex, showing the binding pocket, displaying H-bonds and contacts, measuring key distances, and producing a…
How to Make Publication-Quality Figures in PyMOL: Ray Tracing, Resolution and Journal Requirements 14 min read Beginner to intermediate The gap between a PyMOL screenshot and a journal-ready figure is smaller than most researchers think — but it requires knowing about five or six specific settings that are off by default. This tutorial covers every…
How to Align Protein Structures in PyMOL: align, super and cealign Explained 11 min read Beginner to intermediate Structure alignment is one of the most frequent tasks in structural biology — comparing homologs, validating predictions against experiment, measuring conformational change. PyMOL has three alignment commands, and choosing the wrong one gives misleading RMSD values. This…
How to Show Protein Surfaces in PyMOL: Electrostatics, Hydrophobicity and Binding Pockets 12 min read Beginner to intermediate Surface representations communicate things that cartoon ribbons can’t — the shape of a binding pocket, the electrostatic character of an interface, which patches are hydrophobic. This guide covers every surface type in PyMOL, how to color them…