A collection of star file utilities for Relion 3.0
Convert the beam tilt file name pattern to beam tilt class for Polishing
McGill Krios beam tilt pattern
xxx_micrographNo_HoleId-ShotID.tif
E.g. Micro_00000_1-1.tif, Micro_00003_1-3.tif, Micro_00010_3-2.tif
$python relion3_add_beamtiltclass.py --istar micrographs_ctf.star --ostar micrographs_ctf_beamtiltclass.star --holeno 4
Similar to relion3_add_beamtiltclass.py but now is used for relion 3.1 to accomodate data_optics table. It is tailored to McGill Krios FEMR beam tilt pattern above The script replicates optic groups in data_optic table (indicate by --nogroup) and replaces rlnOpticsGroup in data_particles table with a group number from the micrograph name. Different to the script above, this script using pattern to identify group so it is a bit more robust (McGill pattern _(\d+-\d+).mrc is used as default). It can be best used for micrographs after MotionCorrection or CtfFind. It can also be used for particle file.
$python relion3_1_add_opticgroups.py --istar micrographs_ctf.star --ostar micrographs_ctf_opticgroups.star --nogroup 16
Using a different pattern (Python regex format) $python relion3_1_add_opticgroups.py --istar micrographs_ctf.star --ostar micrographs_ctf_opticgroups.star --nogroup 16 --pattern "_(\d+-\d+).mrc"
Plot the beam tilt estimation from CtfRefine
$python plot_beamtilt_class.py beamtilt_iter-fit_class_*.txt
Output: beamtilt_class.png
Filtering out microtubules with less particles than a threshold
$relion3_0_filter_short_microtubules.py --istar particles.star --ostar particles_filtered.star --minpart 10
Ploting out Phi, Psi, Theta & Shifts for visualization of accurate alignment
$relion3_0_plot_microtubule_alignment.py --istar particles.star --im fit --minpart 10
--im directory to output the graphic
Output: angle plot for each microtubule