Difference between revisions of "Diamond Workshop 2017"
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− | This page | + | 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 | ||
+ | |||
+ | <tt> module load EM/dynamo </tt> | ||
+ | |||
+ | As some visualizations are performed with Chimera you need to activate it as well | ||
+ | |||
+ | <tt> module load chimera </tt> | ||
+ | |||
+ | After ''Dynamo'' and Chimera have been loaded, you can start a session with: | ||
+ | |||
+ | <tt> dynamo </tt> | ||
+ | |||
+ | [[File:dynamo_console.png|thumb|center|800px| Opening the ''Dynamo'' console inside a linux shell with the command <tt>dynamo</tt>]] | ||
+ | |||
+ | === 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=== | ||
+ | |||
+ | [[File:orthoPickMain.png|thumb|upright|250px| Clicking particles in the [[Starters guide ]] ]] | ||
Guided presentation: | Guided presentation: | ||
Line 19: | Line 51: | ||
* Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project. | * Basic [[Starters guide | walkthrough]]: creating a catalogue, picking particles, launching a project. | ||
+ | * [[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. | ||
Line 25: | Line 58: | ||
===Geometric modeling=== | ===Geometric modeling=== | ||
+ | [[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: | ||
Line 35: | Line 69: | ||
Working on your own: | Working on your own: | ||
+ | [[ 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]] ]] | ||
+ | <!--{|style="margin: 0 auto;" | ||
+ | | [[File:HivBox.png|thumb|right|200px| [[Walkthrough for lattices on vesicles | HIV tutorial on densely packed slices]]]] | ||
+ | | [[File:FhvTmsliceUpdates.png|thumb|right|200px| lattice directions ]] | ||
+ | |} --> | ||
+ | * 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) | ||
− | |||
− | |||
− | |||
− | |||
===Template matching=== | ===Template matching=== | ||
Line 47: | Line 84: | ||
[[ 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=== | ||
Line 52: | Line 94: | ||
Short guided presentation: | Short guided presentation: | ||
− | * PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] | + | * PCA [http://{{SERVERNAME}}/w/doc/misc/workshopIntroPCA.pptx Basic concepts.] <br /> advanced subboxing tutorial: combining with PCA and MRA {{pdftutorial|subboxing_multireference_PCA|tutorial}} |
− | * Multirefererence Analysis <br /> [http://{{SERVERNAME}}/w/doc/misc/ | + | * 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 | ||
Line 70: | Line 112: | ||
===Additional tools=== | ===Additional tools=== | ||
− | + | Wednesday afternoon session. | |
− | |||
* 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] | ||
Line 86: | Line 127: | ||
== 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 09:55, 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
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
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:
Geometric modeling
Short guided presentation:
- tutorial on membrane modeling with dmslice
- Filament models with dtmslice
- Reusing model workflows ( walkthrough)
- Further work: catalogue
Working on your own:
- In the afternoon, after the research talks, we will focus on the extraction of particles from densely packed spherical geometry on HIV viral capsides (~1 hour)
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:
- PCA Basic concepts.
advanced subboxing tutorial: combining with PCA and MRA tutorial - Multirefererence Analysis
Basic concepts.
walkthrough (~10 min) - Further work
- Commandline operations with PCA
Creation of 3D scenes
Working on your own:
- Walkthrough on the FHV data set (~1hour)
Further support material.
- Walkthrough on depiction and manipulation of triangulations (synthetic data).
Additional tools
Wednesday afternoon session.
- Subboxing
- motivation slide: extraction of vertices from icosahedral viruses
- Basic subboxing (tutoriall)
- advanced subboxing tutorial: combining with MRA tutorial
- suggested data set: prd1 Capsides (in the folder of isolated particles)
- Manual alignment.
- Exercises
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.