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Tomogram Particle File Reference

WarpTools uses RELION's particle STAR metadata format. This format has changed over time, making users unsure exactly what needs to be in files they provide for particle extraction when using external picking tools.

This page provides examples of metadata that can be used as input to WarpTools ts_export_particles.

  • the list is currently non-exhaustive
  • you can use https://teamtomo.org/starfile/ to read/write these files in Python

RELION 3.0 - single STAR file

data_

loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnCoordinateZ #3
_rlnAngleRot #4
_rlnAngleTilt #5
_rlnAnglePsi #6
_rlnMicrographName #7
443.701994  214.586768  203.739618  54.077932   -29.726951  92.706063   TS_01.tomostar
216.467133  171.667023  157.704667  -168.434232 40.321521   156.800994  TS_01.tomostar
348.701000  91.300066   102.117338  118.892984  -1.043545   127.385870  TS_01.tomostar
465.590176  324.308040  70.420590   105.319824  -37.039451  34.633991   TS_01.tomostar
258.605650  172.224427  97.064928   -74.303821  -3.118226   150.759924  TS_01.tomostar
374.679231  423.019164  205.292795  -130.204570 27.222522   29.593324   TS_02.tomostar
221.453592  425.672254  45.511323   41.711155   48.543276   -82.870213  TS_02.tomostar
348.248079  60.036645   137.823081  123.710065  -86.671079  -34.849912  TS_02.tomostar
229.928165  480.004330  113.754747  -100.103965 165.027964  -76.947619  TS_02.tomostar
385.706010  30.954625   200.434299  26.881529   41.836412   -108.699923 TS_02.tomostar
  • coordinates (required) are interpreted as pixel coordinates in a tomogram, starting from zero at the center of the first voxel
  • rlnMicrographName (optional) should match the tomostar file name for your Warp tilt series processing
  • euler angles (optional) are interpreted as RELION format (ZYZ intrinsic) rotations