Difference between revisions of "Materials Basel 2019"
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===Geometric modeling=== | ===Geometric modeling=== | ||
| − | ''Thursday afternoon''. | + | ''Thursday morning and afternoon''. |
Working on your own: | Working on your own: | ||
| − | * For the | + | * For the Thursday morning session: complete the [[advanced starters guide]] (~2 hours) <br / > the data can be found in <br /><tt> ~/data/crop.rec</tt> <br /> a central file which you can copy is available in <br /> <tt>/clab-share/data/crop.rec</tt> |
| − | * In the afternoon, | + | * In the afternoon, we will focus on the extraction of particles [[Walkthrough for lattices on vesicles| from densely packed spherical geometry ]] (~1 hour) <br /> To get the data, please write in the '''linux terminal''' <br/><tt>'''wget https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec'''</tt> |
Short guided presentation: | Short guided presentation: | ||
| Line 61: | Line 61: | ||
* Further work: catalogue | * Further work: catalogue | ||
| − | === | + | === Fiducial based alignment and reconstruction === |
| + | |||
| + | '''Thursday afternoon after coffee break''' | ||
These new features in ''Dynamo'' are at the testing stage. | 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 === | === Creation of 3D scenes === | ||
| − | + | Friday afternoon. | |
Working on your own: | Working on your own: | ||
Latest revision as of 14:17, 29 August 2019
This page is provided as a generic orientation of the contents of the practical hands-on sessions. Computer access is described here.
Before downloading any workshop data, please check the directory ~/data since most of the needed material is already available there.
Contents
Dynamo version
The current dynamo version is in this file
Matlab crash course
From 9 to 11 a crash course in Matlab will be imparted by Mathworks instructors. The documentation can be opened with:
libreoffice --writer /clab-share/matlabCourse/CrashCourseMATLAB.docx &
Program
The course will start at 11'30 o'clock, Wednesday morning. Last lecture will finish around 12:30 on Friday. On Friday, after lunch, the computer room will be open till 18:00 and our instructors will stay to assist the participants that chose to stay to work with their own data.
Introduction
Wednesday afternoon.
Guided presentation:
- tutorial on basic elements: help, data and metadata formats.
- tutorial on the basic concept in Dynamo alignment: the project.
after the coffee break:
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
Geometric modeling
Thursday morning and afternoon.
Working on your own:
- For the Thursday morning 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
Fiducial based alignment and reconstruction
Thursday afternoon after coffee break
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
Friday afternoon.
Working on your own:
- Walkthrough on the FHV data set (~1hour)
Further support material.
- Walkthrough on depiction and manipulation of triangulations (synthetic data).
Classification
Friday afternoon.
Short guided presentation:
- PCA Basic concepts.
- Multirefererence Analysis
Basic concepts.
walkthrough (~10 min) - Further work
- Commandline operations with PCA
Additional tools and exercises
- Getting a Structure from Multiple Tomograms:
- - In this exercise on VLPs you will be given 6 tomograms of HIV Capsids and the goal is to reach a structure in which alpha helices start to be visible.
- Usage of GPUs
- 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
- Collection of Small Exercises
