Scientific visualization and communication with PyMOL3
Scientific visualization and communication with PyMOL3
5 October 2026, 09h00-17h00
General context
Three-dimensional molecular structures provide critical insight into the function and mechanisms of biological macromolecules. With structural data now widely available, the ability to analyze and clearly communicate these insights is essential.
This hands-on course introduces PyMOL, a leading visualization tool in structural biology. You will learn to load and navigate structures, inspect protein features, apply visualization techniques, and perform basic analyses. A strong focus is on creating clear figures and animations for publications and presentations, helping you illustrate structural features, molecular interactions, and conformational changes effectively.
- Navigate PyMOL interface and organize molecular structures
- Apply different molecular representations, coloring schemes, and display settings
- Identify and examine structural elements such as domains, ligands, and interactions
- Perform basic structural analyses, including measurements of distance, angles, and contacts between atoms and residues
- Create clear and informative molecular figures suitable for scholarly communication
- Create animations and movies to illustrate molecular structures, conformational changes, and interactions
The course combines interactive lectures with hands-on exercises using PyMOL. You will also explore AI-assisted tools to generate commands and Python scripts for advanced visualization and analysis tasks.
- fundamental understanding of biochemistry (especially protein biochemistry)
- familiarity with accessing and retrieving structures from the Protein Data Bank (PDB)
- basic understanding of scripting in Python
- PyMOL3
This course is part of the learning path Structural biology.
AI method used
This course incorporates the use of large language model (LLM) based tools to generate task-specific PyMOL commands that can be executed directly within the PyMOL command line. Participants will also learn how AI-assisted coding tools can be used to develop Python scripts for more advanced visualization and analysis tasks. While these approaches can be used effectively without prior programming experience, a basic understanding of scripting can help users make more efficient use of them and adapt generated solutions to their specific needs.
Trainers
Alexandar Kocev
Alexandar Kocev is a PhD researcher in BioEngineering Sciences at Vrije Universiteit Brussel (VUB), where he focuses on the design and development of Nanobody grafts. With a multidisciplinary background spanning biochemistry, cellular biology, and bioinformatics, he earned a bachelor's degree in biochemistry from Queen's University in Canada, followed by a master's in Biochemistry and Cellular Biology and a second master's degree in Bioinformatics from VU Amsterdam. During his studies, he also completed an internship in Paris, where he developed molecular visualization tools, combining his interests in structural biology, software development, and scientific innovation. Trained in both biochemistry and bioinformatics, he combines experimental life-science expertise with computational methods to tackle challenges in protein engineering and structural biology.
Program
Welcome and set-up
PyMOL introduction and GUI navigation
Coffee break (provided)
Molecular representation and analysis
Lunch (provided)
Figure generation
Coffee break (provided)
Movie making
Wrap-up and discussion
Practical info
05 October 2026
Brussels - Learning & Innovation Center Brussels (LIC)
Pleinlaan 2
1050 Brussels
Belgium
05 October 2026
Brussels - Learning & Innovation Center Brussels (LIC)
05 October 2026
Brussels - Learning & Innovation Center Brussels (LIC)
05 October 2026
Brussels - Learning & Innovation Center Brussels (LIC)
05 October 2026
Brussels - Learning & Innovation Center Brussels (LIC)
Learning & Innovation Center - Pleinlaan 2 -1050 Brussels