dynamo2m

dynamo2m is a small set of tools providing a bidirectional interface between the subtomogram averaging software Dynamo and the Warp-RELION-M pipeline.

A description of the workflow for working between Warp, Dynamo and M can be found here

Motivation

Dynamo is a tomography specific software package with many useful tools for subtomogram averaging including...

• Flexible subtomogram averaging workflows
• Geometric modelling and visualisation tools for particle picking and tomogram annotation
• Automated tilt-series alignment
• Multireference based classification
• PCA based classification and analysis tools
• Interactive tools for initial model generation
• Ways to visualise subtomogram averaging results

M is a software package which allows one to perform multi-particle refinements with the aim of correcting for various sample deformations which can occur during imaging, it currently holds the record for high resolution single particle analysis from frame-series and tilt-series data.

The ability to easily combine these software packages, particularly for particle picking using a modelled supporting geometry, is the goal of the scripts provided in this package.

Scripts

• dynamo2warp for the conversion of Dynamo metadata to facilitate extraction of particles in Warp
• warp2dynamo for the conversion of Warp STAR files into Dynamo compatible metadata
• relion_star_downgrade to convert RELION 3.1 format STAR files into RELION 3.0 format STAR files for extraction in Warp

Installation

Installation is available directly from the Python package index

pip install dynamo2m

Usage

Each of the scripts can be invoked directly from the command line and each has an interactive command line interface.

For example

dynamo2warp

Input Dynamo table file: example.tbl
Input Dynamo table map file: example.doc
Output STAR file: test.star
Done! Converted 'example.tbl' to RELION/Warp/M compatible STAR file 'test_data.star'

Alternatively, options can be passed directly at the command line, this is detailed in the help provided with each script

dynamo2warp --help

Usage: dynamo2warp [OPTIONS]

Options:
  -i, --input_table_file PATH  [required]
  -tm, --table_map_file PATH   [required]
  -o, --output_star_file PATH  [required]
  --help                       Show this message and exit.