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