Reference

PyMOL Wiki

Installing

PyMOL is a commercial project built on an open source foundation. You can download the full commercial product (the incentive version) from pymol.org and, for purposes of learning the software, request a student educational license. However, eventually you will want to install the open source version.

Conda install: conda install conda-forge::pymol-open-source

• Windows install
• Linux install
• Mac install

Learning

• Getting started
• YouTube tutorials
• Tips and Tricks

Creating Figures

• Do not save as an image or (horrors!) take a screenshot. For best results, ray trace the scene and then save the image (using the ray and png commands). Note that newer versions of PyMOL support ray tracing from within the Export Image dialog).
• Set a transparent or white background
• Disable shadows

Selections

• select selection-name, selection-algebra
• i.e. select modified, resname hem+glg+cyp

Alignment

Here is how you align two proteins:

• align mobile, target

Color By Mutation

• First, download the color-by-mutation script here and place it in your current directory.
• In PyMOL, execute the following: run color_by_mutation.py; color_by_mutation protein1, protein2

Example Project

• Fetch PDB 3TU1
• Remove waters
• Color protein with white carbon color scheme
  • Show as cartoon with thin sticks (radius 0.15)
• Color ligand with green carbon color scheme and display as sticks (normal radius)
• Add transparent protein surface (0.2)
• Orient around the ligand
• Find the polar contacts between the ligand and other atoms
• Ray trace and save as 800x600 png