Difference between revisions of "Materials Basel 2018"

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* Further work
 
* Further work
 
** Commandline operations with PCA
 
** Commandline operations with PCA
 
===Exercise: Getting a Structure from Multiple Tomograms===
 
In this exercise 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:
 
* [[Getting_a_Structure_from_Multiple_Tomograms_of_HIV_Capsids|Exercise on VLPs]]
 
For this exercise you also have the opportunity to use the GPUs as described in:
 
* [[GPUs_Basel_2018|Using the GPUs]]
 
  
 
===Additional tools and exercises===
 
===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]
 +
*: - Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l)
 +
*: - advanced subboxing tutorial: combining with MRA  {{pdftutorial|subboxing_multireference_PCA|tutorial}}
 +
*: - suggested data set: prd1 Capsides (in the folder of isolated particles)
 
* Manual alignment
 
* Manual alignment
 
* [[Workshop exercises| Collection of Small Exercises]]
 
* [[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