Difference between revisions of "Diamond Workshop 2017"

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This page is provided as a generic orientation of the contents of the practical hands-on sessions in Diamond (November 2017). The final material will be updated before the beginning of the course.
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This page describes the contents of the practical hands-on sessions in Diamond (28th-29th November 2017).  
  
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Theory will be presented on synthetic data generated on the fly by ''Dynamo''.
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== Computers ==
  
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==Program==
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=== Entering the terminal ===
  
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Exact schedule will be updated here.
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The login and password are written in the front board.
 +
 
 +
=== Starting a ''Dynamo'' session ===
 +
 
 +
''Dynamo'' is already preinstalled in the file system of Diamond.  You can activate it through
 +
 
 +
<tt> module load EM/dynamo </tt>
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 +
As some visualizations are performed with Chimera you need to activate it as well
 +
 
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<tt> module load chimera </tt>
 +
 
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After ''Dynamo'' and Chimera have been loaded, you can start a session with:
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 +
<tt> dynamo </tt>
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[[File:dynamo_console.png|thumb|center|800px| Opening the ''Dynamo'' console inside a linux shell with the command <tt>dynamo</tt>]]
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 +
=== Bringing the data to the local machine ===
 +
 
 +
Some tutorials during the workshop require downloading big files from the ''Dynamo'' wiki using <tt>wget</tt>. You don't need to do that, as they have been already downloaded into the location  <tt>/dls/tmp/DynamoWorkshop/data</tt>, which is visible by all the computers in the workshop.
 +
 
 +
To speed the access to these data sets, it is convenient to make a local copy of them into your own machines. To do so, defore going to lunch, please launch the order:
 +
 
 +
<tt>/dls/tmp/DynamoWorkshop/data/fetchDataToLocalMachine.sh</tt>
 +
 
 +
from a linux shell. This will copy the data into the directory <tt>~/dynamo/data</tt> in your machine.
 +
 
 +
== Program ==
 +
 
 +
Before the hands-on session, we will go to  [http://{{SERVERNAME}}/w/doc/presentations/oxford2017.pptx this presentation] for a general introduction of the ''Dynamo''software.
  
 
===General Introduction===
 
===General Introduction===
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* Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project.
 
* Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project.
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*  [[Advanced starters guide]]  on a real tomogram. (~2 hours)
 
* Further work:
 
* Further work:
 
** {{pdftutorial|commandline|tutorial}} on the use command line operations for general purposes.
 
** {{pdftutorial|commandline|tutorial}} on the use command line operations for general purposes.
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===Geometric modeling===
 
===Geometric modeling===
  
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[[File:membraneExampleCommandLineCroppingPositionsOnMesh.png|thumb|upright|200px| Geometric modeling for [http://{{SERVERNAME}}/w/doc/misc/modelMembrane.pdf surfaces] and [http://{{SERVERNAME}}/w/doc/misc/modelFilament.pdf filaments ]]]
 
Short guided presentation:
 
Short guided presentation:
  
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[[ File:FhvTmsliceUpdates.png |thumb|right|400px|  [[Advanced starters guide | FHV tutorial on isolated membrane events  (advanced starters guide)]]  ]]
 
[[ File:FhvTmsliceUpdates.png |thumb|right|400px|  [[Advanced starters guide | FHV tutorial on isolated membrane events  (advanced starters guide)]]  ]]
 
[[  File:HivBox.png|thumb|right|200px|  [[Walkthrough for lattices on vesicles | HIV tutorial  on densely packed slices]]  ]]
 
[[  File:HivBox.png|thumb|right|200px|  [[Walkthrough for lattices on vesicles | HIV tutorial  on densely packed slices]]  ]]
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<!--{|style="margin: 0 auto;"
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| [[File:HivBox.png|thumb|right|200px| [[Walkthrough for lattices on vesicles | HIV tutorial  on densely packed slices]]]]
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| [[File:FhvTmsliceUpdates.png|thumb|right|200px| lattice directions ]]
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|} -->
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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  on HIV viral capsides]]  (~1 hour)
  
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{|style="margin: 0 auto;"
 
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| [[File:HivBox.png|thumb|upright|200px| [[Walkthrough for lattices on vesicles | HIV tutorial  on densely packed slices]]]]
 
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| [[File:FhvTmsliceUpdates.png|thumb|upright|200px| lattice directions ]]
 
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|}
 
−
 
−
 
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* For the morning session: complete the  [[advanced starters guide]] (~2 hours)
 
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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)
 
 
===Template matching===
 
===Template matching===
  
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[[  File:TemplateMatchingIntoCatalogueZoom.png |thumb|right|400px |  [[Walkthrough for template matching | Template matching]]  ]]
 
[[  File:TemplateMatchingIntoCatalogueZoom.png |thumb|right|400px |  [[Walkthrough for template matching | Template matching]]  ]]
 +
 +
=== Adaptive bandpass filtering ===
 +
 +
Working on your own:
 +
* We will follow this [[Walkthrough on adaptive bandpass filtering| walkthrough]] to create a small synthetic data set that illustrates the principles of [[adaptive bandpass filtering]], a way of conducting a ''golden standard'' alignment procedure . (~40 mins)
  
 
===Classification===
 
===Classification===
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Short guided presentation:
 
Short guided presentation:
  
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* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.]  
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* PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] <br /> advanced subboxing tutorial: combining with PCA and  MRA  {{pdftutorial|subboxing_multireference_PCA|tutorial}}
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* Multirefererence Analysis  <br /> [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx  Basic concepts.]  <br />[[Walkthrough basic multireference|walkthrough]] (~10 min)
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* Multirefererence Analysis  <br /> [http://{{SERVERNAME}}/w/doc/misc/workshopMRAintro.pptx  Basic concepts.]  <br />[[Walkthrough basic multireference|walkthrough]] (~10 min)
 
* Further work
 
* Further work
 
** Commandline operations with PCA
 
** Commandline operations with PCA
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===Additional tools===
 
===Additional tools===
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Friday morning session.
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Wednesday afternoon session.
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* Some tools for tilt series alignment, reconstruction, CTF correction.
 
 
* Subboxing
 
* Subboxing
 
*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
 
*: motivation slide: [http://{{SERVERNAME}}/w/doc/misc/motivationSubboxing.pptx  extraction of vertices from icosahedral viruses]
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== Exercises ==
 
== Exercises ==
 
Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.
 
Exercises are scheduled for the last day. Nevertheless, feel free to start them any time during the workshop.
 +
 +
== Organizers ==
 +
 +
* Tom Burnley, STFC.
 +
* Daniel Castaño-Díez, BioEM Lab, University of Basel.
 +
* Colin Palmer, STFC.
 +
 +
== Instructors ==
 +
 +
*  Daniel Castaño-Díez, University of Basel.
 +
*  Colin Palmer, STFC.
 +
* Paula Navarro, University of Basel.
 +
* Stefano Scaramuzza, University of Basel.

Latest revision as of 10:55, 7 December 2017

This page describes the contents of the practical hands-on sessions in Diamond (28th-29th November 2017).

Computers

Entering the terminal

The login and password are written in the front board.

Starting a Dynamo session

Dynamo is already preinstalled in the file system of Diamond. You can activate it through 

 module load EM/dynamo

As some visualizations are performed with Chimera you need to activate it as well 

 module load chimera

After Dynamo and Chimera have been loaded, you can start a session with: 

 dynamo
Opening the Dynamo console inside a linux shell with the command dynamo

Bringing the data to the local machine

Some tutorials during the workshop require downloading big files from the Dynamo wiki using wget. You don't need to do that, as they have been already downloaded into the location /dls/tmp/DynamoWorkshop/data, which is visible by all the computers in the workshop.

To speed the access to these data sets, it is convenient to make a local copy of them into your own machines. To do so, defore going to lunch, please launch the order: 

/dls/tmp/DynamoWorkshop/data/fetchDataToLocalMachine.sh

from a linux shell. This will copy the data into the directory ~/dynamo/data in your machine.

Program

Before the hands-on session, we will go to this presentation for a general introduction of the Dynamosoftware.

General Introduction

Clicking particles in the Starters guide

Guided presentation:

  • tutorial on basic elements: help, data and metadata formats.
  • tutorial on the basic concept in Dynamo alignment: the project.

Working on your own:

  • Basic walkthrough: creating a catalogue, picking particles, launching a project.
  • Advanced starters guide on a real tomogram. (~2 hours)
  • 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

Geometric modeling for surfaces and filaments

Short guided presentation:

Working on your own:

FHV tutorial on isolated membrane events (advanced starters guide)
HIV tutorial on densely packed slices

Template matching

Working on your own:

  • We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)
Template matching

Adaptive bandpass filtering

Working on your own:

  • We will follow this walkthrough to create a small synthetic data set that illustrates the principles of adaptive bandpass filtering, a way of conducting a golden standard alignment procedure . (~40 mins)

Classification

Short guided presentation:

Creation of 3D scenes

Working on your own:

Scene creation.

Further support material.

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

Additional tools

Wednesday afternoon session.

Data sets

The data sets will be updated here.

Exercises

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

Organizers

  • Tom Burnley, STFC.
  • Daniel Castaño-Díez, BioEM Lab, University of Basel.
  • Colin Palmer, STFC.

Instructors

  • Daniel Castaño-Díez, University of Basel.
  • Colin Palmer, STFC.
  • Paula Navarro, University of Basel.
  • Stefano Scaramuzza, University of Basel.
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