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imod2relion

Python RELION IMOD Open Source

Source

PyPI version [SBGrid software collection]

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

Features Link to this heading

  • 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 Link to this heading

You can install this package by:

bash
1pip install imod2relion

Usage Link to this heading

You can refer to the instructions via:

bash
1imod2relion --help

or

bash
1imod2relion -h

Workflow Link to this heading

Picking particles using IMOD Link to this heading

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 Link to this heading

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

bash
1model2point 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 Link to this heading

bash
1imod2relion --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 Link to this heading

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 Link to this heading

The project is released under the BSD 3-Clause License

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