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 2017 | '''here''']]
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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 2018 | '''here''']].
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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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* 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:
  
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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>
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* 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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* [[Walkthrough on automated marker clicking]]
 
  
 
=== Creation of 3D scenes ===
 
=== Creation of 3D scenes ===
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** Commandline operations with PCA
 
** Commandline operations with PCA
  
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===Additional tools===
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===Additional tools and exercises===
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* Subboxing
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* Getting a Structure from Multiple Tomograms:
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*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
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*: - 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.
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*: Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l)
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* [[GPUs_Basel_2018|Usage of GPUs]]
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*: advanced subboxing tutorial: combining with MRA  {{pdftutorial|subboxing_multireference_PCA|tutorial}}
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* Subboxing:
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*: suggested data set: prd1 Capsides (in the folder of isolated particles)
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*: - motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
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* Manual alignment.
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*: - Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l)
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* [[Workshop exercises| Exercises]]
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*: - advanced subboxing tutorial: combining with MRA  {{pdftutorial|subboxing_multireference_PCA|tutorial}}
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*: - suggested data set: prd1 Capsides (in the folder of isolated particles)
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* Manual alignment
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* [[Workshop exercises| Collection of Small Exercises]]

Latest revision as of 21:43, 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.

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:
    • tutorial on the use command line operations for general purposes.
    • tutorial on the use of the command line to manage projects.

Template matching

Tuesday afternoon.

Working on your own:

Geometric modeling

Working on your own:

Short guided presentation:

Alignment and reconstruction

These new features in Dynamo are at the testing stage.

Creation of 3D scenes

Thursday afternoon.

Working on your own:

Further support material.

  • Walkthrough on depiction and manipulation of triangulations (synthetic data).

Classification

Thursday afternoon.

Short guided presentation:

Additional tools and exercises

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