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imod2relion

PyPI version

A tool reading IMOD points, obtaining particles' info and generating .star file for RELION.

Features

  • Convert txt files containing points' positions into relion star file
  • Directly calculate particles' centers and orientations for further processing in RELION
  • Simplify workflow and make it possible for IMOD picking a small amount of particles manually
  • Generate initial model using IMOD and RELION, especially for membrane proteins

Installation

You can install this package by:

pip install imod2relion

Usage

You can refer to the instructions via:

imod2relion --help

or

imod2relion -h

Workflow

Picking particles using IMOD

You can use IMOD to pick particles, and the information of these particles is determined by selecting two points in sequence in IMOD. This information will be stored in the IMOD model file.

It is worth noting that the position of the particles is calculated as the midpoint of the two points, and the orientation of the particles is calculated as the spatial vector formed by the two points (the first point clicked is the starting point of the vector, and the second point clicked is the endpoint of the vector).

Converting IMOD model into txt files containing positions of points

You can convert an IMOD model to a text file using the following command:

model2point your_tomo_name.mod your_tomo_name.txt

Note that for accuracy in subsequent processing, your text file should be named the same as the tomogram name read in RELION, as the rlnTomoName column in the generated STAR file reads the name of your text file.

Using this tool to generate star file for RELION

imod2relion --input /path/to/txt_files --output /path/to/star/file.star --binning bin_number

  • --input/-i: Path to the directory containing all IMOD .txt files. The .txt filenames must match the tomogram names. This argument is required.

  • --binning/-b: Binning of the tomogram when using IMOD to pick particles. Default is 1.

  • --output/-o: Name of the generated RELION star file. Do not forget the file suffix .star. Default is IMODpoints.star.

Conventions

The conventions used in this script, especially the calculation of Euler angles, are consistent with those used in RELION and in Heymann, Chagoyen and Belnap (2005) standard.

License

The project is released under the BSD 3-Clause License