EMBO workshop 2020
Contents
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
- We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)
The data can be found in
/g/cryocourse/data/dynamo/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
/g/cryocourse/data/dynamo/crop.rec
the chimera path you need in the tutorial is
/g/easybuild/x86_64/CentOS/7/haswell/software/Chimera/1.13-foss-2017b-Python-2.7.14/bin/chimera
- 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).
Submitting jobs For GPU computing
The following is applicable for subtomogram averaging projects setup to be run in the "gpu_standalone" mode under computing environment.
Once your project is unfolded, you should have an executable file
wizardTestProject.exe
The EMBL-HD cluster uses slurm for job submission and resource allocation.
To run this project as a job on their computing resources, we should first set up a submission script, here is an example
#!/bin/bash #SBATCH -N 1 # number of nodes #SBATCH -n 1 # number of cores #SBATCH -o slurm.%N.%j.out # STDOUT #SBATCH -e slurm.%N.%j.err # STDERR #SBATCH --mail-type=END,FAIL # notifications for job done & fail #SBATCH --mail-user=alisterburt@gmail.com # send-to address #SBATCH -p gpu # select gpu usage #SBATCH --gres=gpu:1 # number of gpus (if using gpus) module load dynamo ./wizardTestProject.exe
Save this text file in the same directory as the executable file, then submit the job using sbatch
sbatch dynamo_test_gpu.sl
This should then confirm that the job has been submitted
Submitted batch job 65146729
Submitting jobs for CPU computing
The following is applicable for subtomogram averaging projects setup to be run in the "standalone" mode under computing environment.
Once your project is unfolded, you should have an executable file
wizardTestProject.exe
The EMBL-HD cluster uses slurm for job submission and resource allocation.
To run this project as a job on their computing resources, we should first set up a submission script, here is an example using 6 cores on 1 node
#!/bin/bash #SBATCH -N 1 # number of nodes #SBATCH -n 6 # number of cores #SBATCH -o slurm.%N.%j.out # STDOUT #SBATCH -e slurm.%N.%j.err # STDERR #SBATCH --mail-type=END,FAIL # notifications for job done & fail #SBATCH --mail-user=alisterburt@gmail.com # send-to address module load dynamo ./wizardTestProject.exe
Save this text file in the same directory as the executable file, then submit the job using sbatch
sbatch dynamo_test_cpu.sl
This should then confirm that the job has been submitted
Submitted batch job 65146755
