Cryo EM Solving the Structure of Macromolecular Complexes: A Hands on Workshop

  • Date: Monday, 14 March 2016
  • Venue: 3F, Building for Humanities and Social Science, Academia Sinica
  • Co-organized by: the WeNMR VRC, the MoBrain Competence Center of EGI-Engage and the West-Life VRE project

Description:

Molecular Biology aims at characterizing the mechanisms that take place in the cell. Determining the 3D structure of molecular complexes is crucial to understand their function and inter-relations. 3D electron microscopy (3DEM) has consolidated as a powerful technique to obtain 3D models of the specimen under study by combining information from 2D projection images.

In the last few years we have witnessed a real revolution in the 3DEM field, mainly due to great improvements in equipment, computing power and software tools. The introduction of ``direct detection devices'' (DDDs) has made a fundamental difference in image acquisition quality. Moreover, computer power has increased significantly through the use of multi-core machines, clusters, graphics cards and even the use of cloud computing. All these combined developments have allowed more computationally intensive methods, larger datasets and more challenging biological questions to be posed.

This workshop will provide an introduction to image processing in 3DEM, mainly focused in single particle analysis (SPA). In this technique, we need to deal with several thousands projection images that are "views" of the same specimen under study. The final goal is to determine the spatial 3D orientations of these views and reconstruct a 3D model. A variety of software tools are available to the 3DEM community ranging from command line programs to complete software packages. Each program has its own strengths and weaknesses and no single algorithm performs the best for all situations.

For this workshop we will use Scipion, a new software framework that integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows you to execute workflows combining different tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.

Instructors (in alphabetic order): (To be update)

Program (is subject to update)

09:00 - 10:30
- General introduction to Cryo-EM single particles technique.
- Introduction to Scipion framework

10:30 - 11:00
Coffee break

11:00 - 12:30
- Movies alignment (Xmipp)
- CTF estimation and screening (Ctffind4)
- Particle picking (Xmipp and Eman)

12:30 - 14:00
Lunch

14:00 - 15:30
- 2D classification (Spider)
- More picking with templates (Relion)

15:30 - 16:00
Coffee break

16:00 - 17:30    
- 2D classification (Relion and Xmipp, maybe show precomputed results)
- Initial volume methods (Several packages)
- 3D classification and refinement (Relion, maybe show precomputed results)