Difference between revisions of "Materials Basel 2017"

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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>
 
* 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)
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* 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/hivv/v17.rec'''</tt>
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wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec
  
 
Before going for lunch, please write in a '''linux terminal''':
 
Before going for lunch, please write in a '''linux terminal''':
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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) <br /> To get the data, please write in the '''terminal''' <br/><tt>'''wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc'''</tt>
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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>
  
 
===Classification===
 
===Classification===

Revision as of 12:47, 24 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:

wget https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec

Before going for lunch, please write in a linux terminal:

 /clab-share/bringDataLocal.sh

Template matching

Thursday morning.

Working on your own:

Classification

Friday morning

Short guided presentation:

Creation of 3D scenes

Friday morning

Working on your own:

Further support material.

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

Additional tools

Friday morning 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.