Difference between revisions of "Materials Basel 2017"
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| − | This page is provided as a generic orientation of the contents of the practical hands-on sessions. | + | This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described [[Computers Basel 2017 | '''here''']] |
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==Program== | ==Program== | ||
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Working on your own: | Working on your own: | ||
| − | * For the morning session: complete the [[advanced starters guide]] (~2 hours) | + | * For the morning session: complete the [[advanced starters guide]] (~2 hours) <br / > the data can be found in <br /><tt> ~/data/data/crop.rec</tt> <br /> a central file is available in <br /> <tt>~/clab-share/data/crop.rec</tt> |
| − | * In the afternoon, after the research talks, we will focus on the extraction of particles [[Walkthrough for lattices on vesicles| from densely packed spherical geometry ]] (~1 hour) | + | * In the afternoon, after the research talks, we will focus on the extraction of particles [[Walkthrough for lattices on vesicles| from densely packed spherical geometry ]] (~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/hiv/v17.rec'''</tt> |
===Template matching=== | ===Template matching=== | ||
| − | + | Friday morning. | |
Working on your own: | 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) | + | * 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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=== Creation of 3D scenes === | === Creation of 3D scenes === | ||
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* [[Walkthrough on placement of averages on table positions | Walkthrough ]]on depiction and manipulation of triangulations (synthetic data). | * [[Walkthrough on placement of averages on table positions | Walkthrough ]]on depiction and manipulation of triangulations (synthetic data). | ||
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| + | ===Classification=== | ||
| + | Friday afternoon | ||
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| + | Short guided presentation: | ||
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| + | * 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]] (~10 min) | ||
| + | * Further work | ||
| + | ** Commandline operations with PCA | ||
===Additional tools=== | ===Additional tools=== | ||
| − | Friday | + | Friday afternoon session. |
* Some tools for tilt series alignment, reconstruction, CTF correction. | * Some tools for tilt series alignment, reconstruction, CTF correction. | ||
* Subboxing | * Subboxing | ||
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* Manual alignment. | * Manual alignment. | ||
* [[Workshop exercises| Exercises]] | * [[Workshop exercises| Exercises]] | ||
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== Exercises == | == Exercises == | ||
Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop. | Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop. | ||
Latest revision as of 08:58, 25 August 2017
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.
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:
Geometric 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)
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
Template matching
Friday morning.
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
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).
Classification
Friday afternoon
Short guided presentation:
- PCA Basic concepts.
- Multirefererence Analysis
Basic concepts.
walkthrough (~10 min) - Further work
- Commandline operations with PCA
Additional tools
Friday afternoon 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
Exercises
Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.
