Workshop Description

The overall goal of this workshop is to introduce learners to the kinds of information available about macromolecular structure and how to generate a homology model based on a known structure. The 3 day course will cover; how to access structural data from databases to find a template structure, how to manipulate the data using rosetta and how to view and validate the results using pymol with the end goal being to assess how changes from the template can affect function.

  • Introduction to structure/function relationship
  • Finding a known structure in the PDB using target sequence
  • Explanation of the PDB entry, what different kinds of information can be extracted? Online visualisation tools
  • Downloading PDB file and exploring its contents using command line
  • Different techniques for structure determination and validation metrics
  • Setting up directories for day 2
  • Opening up Python and loading the PyRosetta toolbox
  • Preparing sequence files and PDB files for Comparative modelling
  • Modification in PyRosetta, basic PyRosetta commands
  • Generating multiple homology models potentially using different start points
  • Understanding Rosetta’s scoring system and selecting the best model
  • Visualization using Pymol
  • Different ways to load files into Pymol
  • Different ways to represent structure in Pymol
  • Focusing into and highlighting particular residues
  • Comparison and alignment to known structure(s)
  • Exporting images and movies

Technical Requirements

We have 10 iMac computers with the relevant software installed. If you prefer to bring your own laptop, please installed the following prior to the start of class:

Python (2.7 or 3)
Windows –

Mac – (look at the open source installation)
Windows –
Linux –

Mac (precompiled) –
Windows –

Feel free to come see me in Boyer 529 if you need help installing anything.


To be announced.


Marcus gave a great overarching class that I felt really introduces everyone to the state of the art in protein homology modelling especially with the tools that are available to researchers like pyrosetta. Definitely recommending this course to others.

Marcus was an outstanding instructor! His slides and lectures were incredibly clear, he chose illuminating examples, and he was effective at debugging any small technical issues that came up. I was able to get set up and learn the basics of homology modeling much more quickly and effectively than I could have on my own, and I am leaving the workshop with a clear idea of how to use PyRosetta in my research. Most importantly, I know where to turn to learn even more. 10/10 would recommend

Great introduction to Rosetta and Pymol.

Workshop Details

Required Prerequisites: None
Recommended Prerequisites: W1, W9
Length: 3 days, 2hrs per day
Level: Introductory
Location: Collaboratory Classroom  (Boyer Hall, 529)
Seats Available: 28

Upcoming Dates

Will return Winter 2020.