EMBO workshop 2020

Useful Notes

If at any time after the course you need help with Dynamo/subtomogram averaging, don't hesitate to ask on the [forum in Google Groups]

Instructors

Daniel Castano-Diez - University of Basel

Alister Burt - Institut de Biologie Structurale

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.

• 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

• Further work:
  • tutorial on the use command line operations for general purposes.
  • tutorial on the use of the command line to manage projects.

Day 2

Geometric Modelling

Short guided presentation:

• tutorial on membrane modeling with dmslice
• Filament models with dtmslice
  • tutorial
  • walkthrough
• Reusing model workflows ( walkthrough)
• Further work: catalogue

• In the afternoon, we will focus on the extraction of particles from densely packed spherical geometry (~1 hour)
  

The data is available at

/g/cryocourse/data/dynamo/v17.rec

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

Interfacing with Other Tools

Dynamo is designed to allow maximum user flexibility and to encourage users to design their own solutions to the specific problems posed by their data.

Alister recently spent some time integrating Dynamo with Warp and M to be able to take advantage of Dynamo for tilt-series alignment and particle picking and plug the results into M's multi-particle refinement Integration with Warp and M

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).

Template matching

• 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

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