Difference between revisions of "Materials Basel 2017"
| Line 12: | Line 12: | ||
Wednesday afternoon. | Wednesday afternoon. | ||
| + | |||
| + | Guided presentation: | ||
* [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon] | * [http://{{SERVERNAME}}/w/doc/misc/conceptsSheet.pdf Basic ''Dynamo'' jargon] | ||
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after the coffee break: | after the coffee break: | ||
| + | |||
| + | Working on your own: | ||
* Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project. | * Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project. | ||
| Line 26: | Line 30: | ||
===Data management and modeling=== | ===Data management and modeling=== | ||
| − | Thursday morning | + | |
| + | Thursday morning / afternoon: | ||
| + | |||
| + | Short guided presentation | ||
* [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf tutorial on] membrane modeling with <tt> dmslice </tt> | * [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf tutorial on] membrane modeling with <tt> dmslice </tt> | ||
| Line 34: | Line 41: | ||
* Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]]) | * Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]]) | ||
* Further work: catalogue | * Further work: catalogue | ||
| + | |||
| + | Working on your own: | ||
| + | |||
| + | * For the morning session: complete the [[advanced starters guide]] (~2 hours) | ||
| + | * In the afternoon, after the talks[[Advanced starters guide]] (~1 hour) | ||
| + | |||
| + | ===Template matching=== | ||
| + | |||
| + | Thursday morning. | ||
| + | |||
| + | Working on your own: | ||
| + | |||
| + | * [[Walkthrough for template matching | Walkthrough]] for identification of proteosomes on a real tomogram. (~1 hour) | ||
===Classification=== | ===Classification=== | ||
| − | + | ||
| + | Friday morning | ||
| + | |||
| + | Short guided presentation | ||
| + | |||
* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] | * PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] | ||
* Multirefererence Analysis <br /> [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] <br />[[Walkthrough basic multireference|walkthrough]] | * Multirefererence Analysis <br /> [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] <br />[[Walkthrough basic multireference|walkthrough]] | ||
* Further work | * Further work | ||
** Commandline operations with PCA | ** Commandline operations with PCA | ||
| + | |||
| + | === Creation of 3D scenes === | ||
| + | |||
| + | Friday morning | ||
| + | |||
| + | Working on your own: | ||
| + | |||
| + | * [[Walkthrough on creation of 3d scenes | Walkthrough on the FHV data set]] (~1hour) | ||
| + | |||
| + | Further support material. | ||
| + | |||
| + | * [[Walkthrough on placement of averages on table positions | Walkthrough ]]on depiction and manipulation of triangulations (synthetic data). | ||
===Additional tools=== | ===Additional tools=== | ||
Revision as of 09:41, 22 August 2017
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.
Theory will be presented on synthetic data generated on the fly by Dynamo. Then, the shown theory can be applied on real data sets brought by the participants themselves, or the data sets prepared in the instructor file share under: /Users/gast/mountedData/workshop2017
Contents
Program
The course will start at 10 o'clock, Wednesday morning. Last lecture will finish around 12:30 on Friday. On Friday, after lunch, the computer room will be open till 18:00 and our instructors will stay to assist the participants that chose to stay to work with their own data.
General Introduction
Wednesday afternoon.
Guided presentation:
- 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.
- Further work:
Data management and modeling
Thursday morning / afternoon:
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 talksAdvanced starters guide (~1 hour)
Template matching
Thursday morning.
Working on your own:
- Walkthrough for identification of proteosomes on a real tomogram. (~1 hour)
Classification
Friday morning
Short guided presentation
- PCA Basic concepts.
- Multirefererence Analysis
Basic concepts.
walkthrough - Further work
- Commandline operations with PCA
Creation of 3D scenes
Friday morning
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 tutorial
- advanced subboxing tutorial: combining with MRA (tutoriall)
- suggested data set: prd1 Capsides (in the folder of isolated particles)
- Manual alignment.
- Exercises
Data sets
In the directory /Users/gast/mountedData/workshop2017 there are folders with real data sets representing typical situations. There are both tomograms and already extracted data folders.
- D1 to D4 are tomograms described here.
- D5-D6 are folders containing different formatted data folders.
An additional data set of 5ht3 particles is available through this Google drive link. This data sets includes several thousands of particles. If you want to work with the whole data set, it is a good idea to download it directly into your CSCS account.
Exercises
Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.
