EMBO workshop 2018

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Dynamo will be used for the subtomogram averaging part of the EMBO course on Image Processing for CryoEM data.

Computers

Data sets

In the directory /g/embo2018/data/DYNAMO there are folders with real data sets. Data sets:

  • Tomogram 1 is called crop.rec. The data is a fraction of a tomogram. The full tomogram was used in Cryo-electron tomography reveals novel features of a viral RNA replication compartment. (Ertel et al.), and represents several FHV viruses docked in the outer membrane of a mitochondrion. Data can be downloaded here
  • Tomogram 2 is called t20s.mrc. The tomogram visualises purified T20S proteasome in solution. Data can be downloaded here
  • Tomogram 3 is called v17.rec. This single tomogram is part of the data set used for the paper An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation by Schur FK, Obr M, Hagen WJ, Wan W, Jakobi AJ, Kirkpatrick JM, Sachse C, Kräusslich HG and Briggs JA. (2016). Data can be downloaded here

Program

Tuesday September 4th

General Introduction

Guided presentation:

after the coffee break

Working on your own
  • Basic walkthrough: creating a catalogue, picking particles, launching a project.


Wednesday September 5th

Introduction

Guided presentation:

after the coffee break

Working on your own


Thursday September 6th:

Introduction

Guided presentation
  • Overview discussion with XXX computing modi, with focus on GPUs (EMBO GPUs link).
  • Walkthrough for lattices on vesicles extraction of particles from densely packed spherical geometry.
  • Overview discussion of VLP project.
Working own your own:
  • Walkthrough for VLP project: getting a structure from multiple tomograms of HIV capsids.

Instructors

  • John Briggs, MRC-LMB, Cambridge, UK.
  • Dustin Morado, MRC-LMB, Cambridge, UK.
  • Paula Navarro, C-CINA, University of Basel, Switzerland.
  • Julia Peukes, EMBL, Heidelberg, Germany.
  • Giulia Zanetti, Birkbeck College, London, UK.