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Cryo-ET / Tomography

RECOVAR supports tilt-series data for cryo-ET heterogeneity analysis. One practical advantage over cryoDRGN-ET and tomodrgn is that a focus mask can be used.

Experimental

Cryo-ET support is newer than SPA support and may be less stable. No paper has been published on this feature yet.

Importing from RELION5

If your data was processed in RELION5 (tilt-series alignment + particle extraction), use parse_relion5_tomo to convert to RECOVAR's 2D tilt format:

recovar parse_relion5_tomo \
    -t Polish/job249/tomograms.star \
    -p Extract/job260/particles.star \
    -o particles_2d.star

This reads the RELION5 3D tomography metadata and produces a 2D STAR file where each row is one tilt of one particle, with per-tilt defocus, orientation, and dose information. The output is directly compatible with recovar pipeline --tilt-series.

Requirements:

  • tomograms.star from a Polish or Tomograms job (contains tilt-series geometry)
  • particles.star from an Extract or Refine job (contains 3D particle positions and orientations)

Tilt image dimensions are auto-detected from the MRC headers. Use --tilt-dim W H to override if needed.

Credits

Projection geometry adapted from relion2cryodrgn by Ryan Feathers (Princeton/Zhong lab), based on code by Bogdan Toader (MRC-LMB/RELION team).

Usage

recovar pipeline particles_2d.star -o output \
    --mask mask.mrc --tilt-series

The input is a 2D STAR file with tilt-series metadata (one row per particle per tilt, grouped by _rlnGroupName).

Options

Flag Default Description
--tilt-series False Enable tilt-series mode
--tilt-series-ctf Auto CTF model: cryoem, relion5, warp
--dose-per-tilt From file Dose per tilt in e/A^2
--angle-per-tilt From file Tilt angle increment
--ntilts All Maximum number of tilts to use

CTF models

Model Description
cryoem Standard cryo-EM CTF (for subtomogram averaging)
relion5 RELION 5 tilt-series CTF with dose weighting
warp Warp-style CTF

The default is relion5 for tilt-series data and cryoem otherwise.

With focus mask

A key advantage of RECOVAR for cryo-ET is focus mask support:

recovar pipeline particles.star -o output \
    --mask mask.mrc --focus-mask binding_site.mrc --tilt-series

Tips

  • For cryo-ET data, the --maskrad-fraction default (20) may need adjustment. Lower-resolution data may benefit from increasing this value.
  • The --n-min-particles default (100) may need to be reduced for smaller tomography datasets.
  • Use --ntilts to limit the number of tilts if some have poor quality.