Getting started with ChimeraX

This is an introductory tutorial to UCSF ChimeraX, written for people who are new to the software. It was originally developed to help train colleagues whose research backgrounds were primarily in genetics rather than structural biology, with the aim of getting them comfortable visualising and interpreting AlphaFold predictions of their proteins of interest.

The tutorial assumes no prior knowledge of ChimeraX. It begins with opening the software and loading a model, and works through the core features needed for day to day structure analysis: model manipulation and selection syntax, visualising contacts and interfaces, colouring schemes, superposing structures, generating publication quality images, making simple movies, and analysing AlphaFold models (including the predicted aligned error plot and predicted contacts). The worked examples use PDB entries 7PP2 and 2PFT, but every section is written so that users can substitute in their own structures and follow along.

The tutorial takes approximately 1.5 hours to complete in full. It is intended as both a standalone self study resource and a teaching aid, and may be used freely in undergraduate or postgraduate courses, lab meetings, or for individual reference.

ChimeraX is developed and maintained by the Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco, with support from NIH R01 GM129325. I am very grateful to the ChimeraX team for building and freely distributing such an excellent piece of software. If you use ChimeraX in published work, please cite Meng et al. (2023) Protein Science (doi:10.1002/pro.4792) alongside any citation of this tutorial.

I intend to keep this resource updated as ChimeraX evolves. Questions, corrections and suggestions are very welcome.