Difference between revisions of "EMBO workshop 2018"
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== Data sets == | == Data sets == | ||
| − | In the directory <tt> | + | In the directory <tt>/g/embo2018/data/DYNAMO</tt> there are folders with real data sets. Data sets: |
| − | *Tomogram 1 is called <tt>crop.rec</tt>. The data is a fraction of a tomogram. The full tomogram was used in | + | *Tomogram 1 is called <tt>crop.rec</tt>. 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 [[Advanced_starters_guide#Downloading | here]] |
*Tomogram 2 is called <tt>t20s.mrc</tt>. The tomogram visualises purified T20S proteasome in solution. Data can be downloaded [[Walkthrough_for_template_matching#Data_set | here]] | *Tomogram 2 is called <tt>t20s.mrc</tt>. The tomogram visualises purified T20S proteasome in solution. Data can be downloaded [[Walkthrough_for_template_matching#Data_set | here]] | ||
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| + | *Tomogram 3 is called <tt>v17.rec</tt>. 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 [[Walkthrough_for_lattices_on_vesicles#Data | here]] | ||
==Program== | ==Program== | ||
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=====Guided presentation:===== | =====Guided presentation:===== | ||
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* Walkthrough on [[Walkthrough_for_template_matching | template matching]] | * Walkthrough on [[Walkthrough_for_template_matching | template matching]] | ||
* Overview discussion of [[Advanced_starters_guide | Advanced starters guide]] | * Overview discussion of [[Advanced_starters_guide | Advanced starters guide]] | ||
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=====Working on your own===== | =====Working on your own===== | ||
* Walkthrough for [[Advanced_starters_guide | Advanced starters guide]] | * Walkthrough for [[Advanced_starters_guide | Advanced starters guide]] | ||
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| + | |||
===Thursday September 6th:=== | ===Thursday September 6th:=== | ||
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=====Working own your own:===== | =====Working own your own:===== | ||
| − | *VLP project | + | *Walkthrough for [[Getting_a_Structure_from_Multiple_Tomograms_of_HIV_Capsids_(walkthrough) | VLP project]]: getting a structure from multiple tomograms of HIV capsids. |
| + | ==Instructors== | ||
| − | + | *John Briggs, MRC-LMB, Cambridge, UK. | |
*Dustin Morado, MRC-LMB, Cambridge, UK. | *Dustin Morado, MRC-LMB, Cambridge, UK. | ||
*Paula Navarro, C-CINA, University of Basel, Switzerland. | *Paula Navarro, C-CINA, University of Basel, Switzerland. | ||
| + | |||
| + | *Julia Peukes, EMBL, Heidelberg, Germany. | ||
* Giulia Zanetti, Birkbeck College, London, UK. | * Giulia Zanetti, Birkbeck College, London, UK. | ||
Latest revision as of 08:01, 5 September 2018
Dynamo will be used for the subtomogram averaging part of the EMBO course on Image Processing for CryoEM data.
Contents
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:
- Basic Dynamo jargon
- tutorial on basic elements: help, data and metadata formats.
- tutorial on the basic concept in Dynamo alignment: the project.
after the coffee break
Working on your own
- Basic walkthrough: creating a catalogue, picking particles, launching a project.
Wednesday September 5th
Introduction
Guided presentation:
- Walkthrough on template matching
- Overview discussion of Advanced starters guide
after the coffee break
Working on your own
- Walkthrough for Advanced starters guide
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.
