Difference between revisions of "Materials Basel 2018"
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** {{pdftutorial|commandline|tutorial}} on the use command line operations for general purposes. | ** {{pdftutorial|commandline|tutorial}} on the use command line operations for general purposes. | ||
** {{pdftutorial|command_line_projects|tutorial}} on the use of the command line to manage projects. | ** {{pdftutorial|command_line_projects|tutorial}} on the use of the command line to manage projects. | ||
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| + | ===Template matching=== | ||
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| + | Tuesday afternoon. | ||
| + | |||
| + | Working on your own: | ||
| + | |||
| + | * We will follow this [[Walkthrough for template matching | walkthrough]] for automated identification of proteosomes on a real tomogram through template matching. (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/><tt>'''wget https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc'''</tt> | ||
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===Geometric modeling=== | ===Geometric modeling=== | ||
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* Further work: catalogue | * Further work: catalogue | ||
| − | === | + | === Alignment and reconstruction === |
| − | |||
| − | |||
| − | + | These new features in ''Dynamo'' are at the testing stage. | |
| − | * | + | * [[Walkthrough on manual marker clicking ]] |
| + | * [[Walkthrough on automated marker clicking]] | ||
=== Creation of 3D scenes === | === Creation of 3D scenes === | ||
| − | + | Thursday afternoon. | |
Working on your own: | Working on your own: | ||
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===Classification=== | ===Classification=== | ||
| − | + | Thursday afternoon. | |
Short guided presentation: | Short guided presentation: | ||
| Line 70: | Line 78: | ||
===Additional tools=== | ===Additional tools=== | ||
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* Subboxing | * Subboxing | ||
*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx extraction of vertices from icosahedral viruses] | *: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx extraction of vertices from icosahedral viruses] | ||
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* Manual alignment. | * Manual alignment. | ||
* [[Workshop exercises| Exercises]] | * [[Workshop exercises| Exercises]] | ||
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Revision as of 14:41, 23 August 2018
This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described here
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.
Geometric modelling
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:
Template matching
Tuesday afternoon.
Working on your own:
- We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)
To get the data, please write in the linux terminal
wget https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc
Geometric modeling
Working on your own:
- For the morning session: complete the advanced starters guide (~2 hours)
the data can be found in
~/data/data/crop.rec
a central file is available in
~/clab-share/data/crop.rec - In the afternoon, after the research talks, we will focus on the extraction of particles from densely packed spherical geometry (~1 hour)
To get the data, please write in the linux terminal
wget https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec
Short guided presentation:
- tutorial on membrane modeling with dmslice
- Filament models with dtmslice
- Reusing model workflows ( walkthrough)
- Further work: catalogue
Alignment and reconstruction
These new features in Dynamo are at the testing stage.
Creation of 3D scenes
Thursday afternoon.
Working on your own:
- Walkthrough on the FHV data set (~1hour)
Further support material.
- Walkthrough on depiction and manipulation of triangulations (synthetic data).
Classification
Thursday afternoon.
Short guided presentation:
- PCA Basic concepts.
- Multirefererence Analysis
Basic concepts.
walkthrough (~10 min) - Further work
- Commandline operations with PCA
Additional tools
- 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
