Difference between revisions of "Diamond Workshop 2017"
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| − | This page is provided as a generic orientation of the contents of the practical hands-on sessions. The final material will be updated before the beginning of the course. | + | This page is provided as a generic orientation of the contents of the practical hands-on sessions in Diamond (November 2017). The final material will be updated before the beginning of the course. |
Theory will be presented on synthetic data generated on the fly by ''Dynamo''. | Theory will be presented on synthetic data generated on the fly by ''Dynamo''. | ||
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==Program== | ==Program== | ||
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===General Introduction=== | ===General Introduction=== | ||
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Guided presentation: | Guided presentation: | ||
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* [http://{{SERVERNAME}}/w/doc/misc/introductionTablesAndData.pdf tutorial on] basic elements: help, data and metadata formats. | * [http://{{SERVERNAME}}/w/doc/misc/introductionTablesAndData.pdf tutorial on] basic elements: help, data and metadata formats. | ||
* [http://{{SERVERNAME}}/w/doc/misc/introductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. | * [http://{{SERVERNAME}}/w/doc/misc/introductionAlignmentProjects.pdf tutorial on] the basic concept in ''Dynamo'' alignment: the ''project''. | ||
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Working on your own: | Working on your own: | ||
Revision as of 08:12, 23 August 2017
This page is provided as a generic orientation of the contents of the practical hands-on sessions in Diamond (November 2017). The final material will be updated before the beginning of the course.
Theory will be presented on synthetic data generated on the fly by Dynamo.
Contents
Program
Exact schedule will be updated here.
General Introduction
Guided presentation:
- tutorial on basic elements: help, data and metadata formats.
- tutorial on the basic concept in Dynamo alignment: the project.
Working on your own:
- Basic walkthrough: creating a catalogue, picking particles, launching a project.
- Further work:
Geometric modeling
Short guided presentation:
- tutorial on membrane modeling with dmslice
- Filament models with dtmslice
- Reusing model workflows ( walkthrough)
- Further work: catalogue
Working on your own:
- For the morning session: complete the advanced starters guide (~2 hours)
- In the afternoon, after the research talks, we will focus on the extraction of particles from densely packed spherical geometry (~1 hour)
Template matching
Working on your own:
- We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)
Classification
Short guided presentation:
- PCA Basic concepts.
- Multirefererence Analysis
Basic concepts.
walkthrough (~10 min) - Further work
- Commandline operations with PCA
Creation of 3D scenes
Working on your own:
- Walkthrough on the FHV data set (~1hour)
Further support material.
- Walkthrough on depiction and manipulation of triangulations (synthetic data).
Additional tools
Friday morning session.
- Some tools for tilt series alignment, reconstruction, CTF correction.
- Subboxing
- motivation slide: extraction of vertices from icosahedral viruses
- Basic subboxing (tutoriall)
- advanced subboxing tutorial: combining with MRA tutorial
- suggested data set: prd1 Capsides (in the folder of isolated particles)
- Manual alignment.
- Exercises
Data sets
The data sets will be updated here.
Exercises
Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.
