Difference between revisions of "Materials Basel 2018"
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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. | 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: | Guided presentation: | ||
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===Geometric modeling=== | ===Geometric modeling=== | ||
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| + | Working on your own: | ||
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| + | * 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) <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> | ||
Short guided presentation: | Short guided presentation: | ||
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* Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]]) | * Reusing model workflows ([[Walkthrough model worfklow reuse | walkthrough]]) | ||
* Further work: catalogue | * Further work: catalogue | ||
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===Template matching=== | ===Template matching=== | ||
Revision as of 11:06, 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:
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
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.
