Learning to visualise and analyse molecular structures with ChimeraX

Renato Alves   2023-04-19   Comments Off on Learning to visualise and analyse molecular structures with ChimeraX

Date(s) - 2023-04-19
14:00 CEST - 17:00 CEST


Instructors / helpers

  • Toby Gibson
  • Manjeet Kumar
  • Jesús Alvarado Valverde
  • Renato Alves


This 3 hour afternoon course will be held both in person and online (hybrid).

In this course, we will explore UCSF ChimeraX for the visualizaton of protein structures.
You will be introduced to different structural formats (PDB, PDBx/mmCIF) and learn how to load them from local files or directly from RCSB PDB, PDBe and AlphaFold.

You will also learn how to use the different visualisation modes (ribbons, sidechains, surfaces, hydrogen bonds, etc.) and the sequence editor to highlight biological features and regions of interest. You will be able to compare related structures through structure superposition, inspect surfaces and infer functional implications from topological features, binding interfaces and sequence conservation.
Finally, you will be able able to produce publication quality images for small and large protein complexes.


Session 1: Introduction to ChimeraX

  • Protein visualization background
  • Resources for learning
  • File formats (PDB & mmCIF)
  • Opening a structure, various visualizations
  • Generating publication quality figures

Session 2: Structural alignments and analyses

  • Hybrid visualizations (Domain-peptide, protein-DNA)
  • Aligning structures
  • Visualizing binding sites, conservation, hydrogen bonds and other biological features

Session 3: ChimeraX advanced

  • Visualizing large macromolecular complexes
  • Making molecular movies
  • Integrating other resources
  • Using AlphaFold2 for structure modeling
  • Cytoscape

Preparation in Advance

Preinstall and briefly test on your laptop:


EMBL Bio-IT and the Gibson Team will offer the course for free to all EMBL members.

The course is limited to 20 in-person (in Heidelberg) seats which shall be allocated on a first come first served basis.

Registration deadline: Friday, 14th April 2023 – 17:00


Bookings are closed for this event.

About Renato Alves

I am a Community and Project Manager for Bio-IT and Training Coordinator for ELIXIR Germany. Find me at EMBL-HD office 116 or at Bio-IT drop-in Sessions on Tuesdays 10:00-12:00 at the EMBL staff lounge (or online). Contact Details: email - renato.alves@embl.de, Twitter - https://twitter.com/renato_alvs, GitHub - https://github.com/unode, GitLab - https://gitlab.com/unode, ORCID - https://orcid.org/0000-0002-7212-0234