Difference between revisions of "Materials Basel 2017"

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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>
  
===Classification===
 
 
Friday morning
 
 
Short guided presentation:
 
 
* 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
 
  
 
=== 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).
 +
 +
 +
===Classification===
 +
Friday afternoon
 +
 +
Short guided presentation:
 +
 +
* 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 morning session.
+
Friday afternoon session.
 
* Some tools for tilt series alignment, reconstruction, CTF correction.
 
* Some tools for tilt series alignment, reconstruction, CTF correction.
 
* Subboxing
 
* Subboxing

Revision as of 08:57, 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

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

Geometric modeling

Thursday morning / afternoon.

Short guided presentation:

Working on your own:

Template matching

Thursday morning.

Working on your own:


Creation of 3D scenes

Friday morning

Working on your own:

Further support material.

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


Classification

Friday afternoon

Short guided presentation:

Additional tools

Friday afternoon session.

Data sets

In the directory /Users/gast/mountedData/workshop2017 there are folders with real data sets representing typical situations. There are both tomograms and already extracted data folders.

  • D1 to D4 are tomograms described here.
  • D5-D6 are folders containing different formatted data folders.

An additional data set of 5ht3 particles is available through this Google drive link. This data sets includes several thousands of particles. If you want to work with the whole data set, it is a good idea to download it directly into your CSCS account.

Exercises

Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.