EMBO workshop 2020

From Dynamo
Jump to navigation Jump to search


Day 1

Basic principles

Guided presentation:

Working on your own:

  • Basic walkthrough: creating a catalogue, picking particles, launching a project.
  • Further work:
    • tutorial on the use command line operations for general purposes.
    • tutorial on the use of the command line to manage projects.

Template matching

Wednesday afternoon.

Working on your own:

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

Short guided presentation:

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:

Further support material.

  • Walkthrough on depiction and manipulation of triangulations (synthetic data).

Submitting jobs For GPU computing

This 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


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

#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

Save this text file in the same directory as the executable file, then submit the job using sbatch

sbatch dynamo_test.sl 

This should then confirm that the job has been submitted

Submitted batch job 65146729