EMBO workshop 2020
Revision as of 08:09, 6 August 2020 by Daniel Castaño (talk | contribs)
Materials
Day 1
Basic principles
Guided presentation:
- Basic Dynamo jargon
- 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.
- Further work:
Template matching
Wednesday afternoon.
Working on your own:
- We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)
To get the data, please write in the linux terminal
wget https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/t20s/t20s.mrc
Day 2
Geometric modeling
Working on your own:
- For the Day 2 session: complete the advanced starters guide (~2 hours)
the data can be found in
~/data/crop.rec
a central file which you can copy is available in
/clab-share/data/crop.rec - In the afternoon, we will focus on the extraction of particles from densely packed spherical geometry (~1 hour)
To get the data, please write in the linux terminal
wget https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec
Short guided presentation:
- tutorial on membrane modeling with dmslice
- Filament models with dtmslice
- Reusing model workflows ( walkthrough)
- Further work: catalogue
Day 3
Fiducial based alignment and reconstruction
These new features in Dynamo are at the testing stage.
GUI based alignment of tilt series
Walkthrough on GUI based tilt series alignment
Command line based alignment of tilt series
Walkthrough on command line based tilt series alignment
Manual clicking on gold beads
Walkthrough on manual marker clicking
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).
