Difference between revisions of "Dynamo Workshop at the International School of Crystallography 2019"

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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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This page describes the contents of the practical hands-on sessions for tomography through ''Dynamo''  in at the 54th International School of Crystallography in Erice.
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A core presentation will be held on site
  
== Computers ==
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== Installing Dynamo ==
  
=== Entering the terminal ===
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=== Donwload ===
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The Dynamo versions on the three platforms can be obtained in the [[Downloads]] page. Please use the indications [[Installation|here]] to install it in your laptop.
  
The login and password are written in the front board.
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=== Starting a ''Dynamo'' session ===
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You need to run an activation shell (see below for information on how to do it on each platform)  that can  be used to run [[alignment project]]s or to initiate an interactive session using the ''Dynamo'' [[Dynamo console|console]]. For this, you can just type:
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<tt>dynamo </tt>
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on a ''Dynamo''-activated system shell  and be patient: the first time a shell initiates a ''Dynamo'' process, it can takes several minutes. New invocations to the MCR libraries will be much faster, and commands inside the opened ''Dynamo'' session will run immediately.
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==== Linux ====
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On a  Linux terminal, type:
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<tt> source <DYNAMO_ROOT>/dynamo_activate_linux_with_shippedMRC.sh</tt>
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==== Mac ====
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On a  Mac termina, type:
  
=== Starting a ''Dynamo'' session ===
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<tt> source <DYNAMO_ROOT>/dynamo_activate_mac_with_shippedMRC.sh</tt>
  
''Dynamo'' is already preinstalled in the file system of Diamond. You can activate it through
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==== Windows ====
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In a DOS terminal write:
  
  <tt> module load EM/dynamo </tt>
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  <tt>C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat </tt>
  
As some visualizations are performed with Chimera you need to activate it as well
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then open a ''Dynamo'' terminal by typing in the DOS
  
  <tt> module load chimera </tt>
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  <tt>dynamo</tt>
  
After ''Dynamo'' and Chimera have been loaded, you can start a session with:
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If it doesn't work, type:
  
  <tt> dynamo </tt>
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  <nowiki> set PATH=%PATH%;%MCR_ROOT%\runtime\win64</nowiki>
  
[[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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and then '''again'''
  
=== Bringing the data to the local machine ===
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<tt>C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat </tt>
  
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:
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=== Running a ''Dynamo'' project in the standalone ===
  
<tt>/dls/tmp/DynamoWorkshop/data/fetchDataToLocalMachine.sh</tt>  
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When working with the standalone, it is '''not''' convenient to run projects directly pressing [Run] in the <tt>dcp</tt> GUI. It is a better approach to run the project in a different process.
  
from a linux shell. This will copy the data into the directory <tt>~/dynamo/data</tt> in your machine.
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* Open a new system shell (DOS shell in windows).
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* Activate ''Dynamo'' in that shell. i.e.,
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**Linux: <tt> source <DYNAMO_ROOT>/dynamo_activate_linux_with_shippedMRC.sh</tt>
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* Do '''NOT''' start a ''Dynamo'' session, i.e., do not type <tt>dynamo</tt> in the shell.
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* In the terminal, type the name of the execution script.
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** Linux/Mac:  <tt>./ptest.exe</tt>
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** Windows: <tt>./ptest.bat</tt>
  
 
== Program ==
 
== Program ==

Latest revision as of 14:17, 5 June 2019

This page describes the contents of the practical hands-on sessions for tomography through Dynamo in at the 54th International School of Crystallography in Erice. A core presentation will be held on site

Installing Dynamo

Donwload

The Dynamo versions on the three platforms can be obtained in the Downloads page. Please use the indications here to install it in your laptop.

Starting a Dynamo session

You need to run an activation shell (see below for information on how to do it on each platform) that can be used to run alignment projects or to initiate an interactive session using the Dynamo console. For this, you can just type:

dynamo 

on a Dynamo-activated system shell and be patient: the first time a shell initiates a Dynamo process, it can takes several minutes. New invocations to the MCR libraries will be much faster, and commands inside the opened Dynamo session will run immediately.

Linux

On a Linux terminal, type:

 source <DYNAMO_ROOT>/dynamo_activate_linux_with_shippedMRC.sh

Mac

On a Mac termina, type:

 source <DYNAMO_ROOT>/dynamo_activate_mac_with_shippedMRC.sh

Windows

In a DOS terminal write:

C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat 

then open a Dynamo terminal by typing in the DOS

dynamo

If it doesn't work, type:

 set PATH=%PATH%;%MCR_ROOT%\runtime\win64

and then again

C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat


Running a Dynamo project in the standalone

When working with the standalone, it is not convenient to run projects directly pressing [Run] in the dcp GUI. It is a better approach to run the project in a different process.

  • Open a new system shell (DOS shell in windows).
  • Activate Dynamo in that shell. i.e.,
    • Linux: source <DYNAMO_ROOT>/dynamo_activate_linux_with_shippedMRC.sh
  • Do NOT start a Dynamo session, i.e., do not type dynamo in the shell.
  • In the terminal, type the name of the execution script.
    • Linux/Mac: ./ptest.exe
    • Windows: ./ptest.bat

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:

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)

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:

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.



Instructors

  • Daniel Castaño-Díez, University of Basel.