DiMaio Lab

Institute for Protein Design
University of Washington


Model-building and refinement into cryoEM density

Our cryoEM model-building and refinement tools are included as part of the Rosetta software package. Rosetta includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

Rosetta is available to all non-commercial users for free and to commercial users for a fee. Visit rosettacommons.org to learn more.


Our lab participated in the 2019 Model Metrics Challenge.

We have provided command lines for all of our entries.
[README][all files (tgz)]


Using Rosetta with cryoEM density (last updated August 2018)
This tutorial gives an overview of all the EM-related tools available within Rosetta.
[instructions (pdf)] [all files (tgz)]

You may also download sections individually:

  • Part 1: Introduction to Rosetta for cryoEM  [pdf][tgz]
  • Part 2: Fragment-based structure refinement [pdf][tgz]
  • Part 3: Model rebuilding using RosettaCM [pdf][tgz]
  • Part 4: De novo EM-guided structure determination [pdf][tgz]
  • Part 5: Rebuilding long protein segments with RosettaES [pdf][tgz]

A tutorial given at EMBL in August 2022
This tutorial features new examples.[instructions (pdf)] [all files (tgz)][slides (pdf)]

A modified tutorial given at CSHL in March 2019
This somewhat simplified tutorial mostly focuses on RosettaCM with a few new examples.[instructions (pdf)] [all files (tgz)]


Supplemental Materials from Wang et al., eLife 2016 [1][2][3]