EPU beam tilt classes

A simple (updated) script that uses the third position in the EPU micrograph file name (e.g., FoilHole_10218182_Data_10216707_10216709_20231010_225333_fractions.tiff) for beam tilt class. The script updates the optics part of the Relion 3+ data star file and saves a new modified star. Whether this modification affects the resolution is yet to be determined.

Requirements

• Python
• Particle star file
• EPU recorded micrographs that have the original name
• In case for cryoSPARC, write access to the directory

Included:

Python script and Jupyter Notebook.

Not tested:

• Initial multiple optic groups
• ?

Usage:

Relion 3+: python find_beamtilt_classes.py --i /mnt/gpu_scratch/Extract/job027/particles.star --o /mnt/gpu_scratch/Extract/job027/particles_beamtilt.star

cryoSPARC: python find_beamtilt_classes_cs.py --i /mnt/hdd/CS-project/J835/J835_005_particles.cs cryoSPARC version of this script replaces the cs file indicated and creates a backup. This does not require anything extra from the GUI; just run Global CTF and enjoy!

Requirements:

pip install pandas gemmi numpy

Proof-of-Principle

X and Y values obtained from XML files

Color from the 3rd number in the EPU

cryoSPARC support:

Author:

Dawid Zyla, La Jolla Institute for Immunology