Difference between revisions of "''Dynamo''workshop at the New York Structural Biology Center 2016"
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* 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] | ||
− | *: Basic subboxing {{pdftutorial| | + | *: Basic subboxing ({{pdftutorial|subboxing_symmetry|tutorial}}l) |
− | *: advanced subboxing tutorial: combining with MRA | + | *: advanced subboxing tutorial: combining with MRA{{pdftutorial|subboxing_multireference_PCA|tutorial}} |
*: suggested data set: prd1 Capsides (in the folder of isolated particles) | *: suggested data set: prd1 Capsides (in the folder of isolated particles) | ||
* Manual alignment. | * Manual alignment. |
Latest revision as of 16:09, 9 December 2016
The NYSBC offer a two-day compact course on the use of the Dynamo software for subtomogram averaging and tomography. This workshop provides hands-on training in all practical aspects of sub-tomogram averaging, encompassing all stages of the pipeline: tomogram visualization and archiving, particle picking, averaging, refinement and classification. No previous experience will be required.
An additional day will be offered for those interested in deepening the topics presented during the first two days.
Contents
Registration
To be announced.
Requirements
Participants are welcome to bring along their own laptops.
Dynamo can be run as standalone (in Linux) or inside the commercial Matlab software (Linux or Mac). For this course, we ask participants to get beforehand a trial license for Matlab. Please, perform the installation of the latest version of Dynamo on your laptop before the course.
Also, we encourage participants to check beforehand if they have access to GPU machines through their home institution.
Program
This program is provisional.
Introduction: alignment projects
- tutorial on basic elements: help, data and metadata formats.
- tutorial on the basic concept in Dynamo alignment: the project.
after the coffee break:
- Basic walkthrough: creating a catalogue, picking particles, launching a project.
- Further work:
Data management and modeling
- tutorial on membrane modeling with dmslice
- Filament models with dtmslice
- Reusing model workflows ( walkthrough)
- Further work: catalogue
Classification
- PCA Basic concepts.
- Multirefererence Analysis
Basic concepts.
walkthrough - Further work
- Commandline operations with PCA
Additional tools
We offer an extra day for those interested in working with their own data, or discussing with the instructors more advanced topics.
- Subboxing
- motivation slide: extraction of vertices from icosahedral viruses
- Basic subboxing (tutoriall)
- advanced subboxing tutorial: combining with MRAtutorial
- suggested data set: prd1 Capsides (in the folder of isolated particles)
- Manual alignment.
- Exercises
Organizers
Alex Noble, NYSBC, New York.
Instructors
- Alex Noble, NYSBC, New York.
- Daniel Castaño-Díez, BioEM lab, Biozentrum, University of Basel.