Difference between revisions of "Materials Basel 2018"
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| − | This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described [[Computers Basel | + | This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described [[Computers Basel 2018 | '''here''']]. |
| + | |||
| + | Before downloading any workshop data, please check the directory <tt>~/data</tt> since most of the needed material is already available there. | ||
==Program== | ==Program== | ||
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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. | ||
| − | === | + | === Introduction === |
Guided presentation: | Guided presentation: | ||
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* 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> | * 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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Working on your own: | Working on your own: | ||
| − | * For the morning session: complete the [[advanced starters guide]] (~2 hours) <br / > the data can be found in <br /><tt> ~ | + | * For the Wednesday morning session: complete the [[advanced starters guide]] (~2 hours) <br / > the data can be found in <br /><tt> ~/data/crop.rec</tt> <br /> a central file which you can copy 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> | * 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> | ||
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* [[Walkthrough on manual marker clicking ]] | * [[Walkthrough on manual marker clicking ]] | ||
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=== Creation of 3D scenes === | === Creation of 3D scenes === | ||
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** Commandline operations with PCA | ** Commandline operations with PCA | ||
| − | ===Additional tools=== | + | ===Additional tools and exercises=== |
| − | * Subboxing | + | * Getting a Structure from Multiple Tomograms: |
| − | *: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx extraction of vertices from icosahedral viruses] | + | *: - In this [[Getting_a_Structure_from_Multiple_Tomograms_of_HIV_Capsids|exercise on VLPs]] you will be given 6 tomograms of HIV Capsids and the goal is to reach a structure in which alpha helices start to be visible. |
| − | *: Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l) | + | * [[GPUs_Basel_2018|Usage of GPUs]] |
| − | *: advanced subboxing tutorial: combining with MRA {{pdftutorial|subboxing_multireference_PCA|tutorial}} | + | * Subboxing: |
| − | *: suggested data set: prd1 Capsides (in the folder of isolated particles) | + | *: - motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx extraction of vertices from icosahedral viruses] |
| − | * Manual alignment | + | *: - Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l) |
| − | * [[Workshop exercises| Exercises]] | + | *: - advanced subboxing tutorial: combining with MRA {{pdftutorial|subboxing_multireference_PCA|tutorial}} |
| + | *: - suggested data set: prd1 Capsides (in the folder of isolated particles) | ||
| + | * Manual alignment | ||
| + | * [[Workshop exercises| Collection of Small Exercises]] | ||
Latest revision as of 22:43, 29 August 2018
This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described here.
Before downloading any workshop data, please check the directory ~/data since most of the needed material is already available there.
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.
Introduction
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 Wednesday morning session: complete the advanced starters guide (~2 hours)
the data can be found in
~/data/crop.rec
a central file which you can copy 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 and exercises
- Getting a Structure from Multiple Tomograms:
- - In this exercise on VLPs you will be given 6 tomograms of HIV Capsids and the goal is to reach a structure in which alpha helices start to be visible.
- Usage of GPUs
- 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
- Collection of Small Exercises
