cryoEF: Efficiency of cryo-EM reconstruction

In order to validate and analyze the orientation distribution for a given reconstruction, Chris Russo and co-workers developed a measurement called ‘Efficiency’ (or cryoEF). CryoEF provides a direct measure of the particle distribution for a given 3D reconstruction.

Original publication: Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy

Documentation webpage

Why should you use this?

CryoEF provides you with a direct measure of the reliability of your reconstruction. If you are missing too many views for a given reconstruction, this anisotropy of particles will lead to ‘streakiness’ in the map which will affect interpretation and model building.

cryoEF values >0.8 are typically associated with reliable reconstructions

Predicting tilt angle for datasets with preferred orientations

Another feature of cryoEF that is useful relates to its ability to provide recommended tilt angles and particle numbers in order to overcome any preferred orientations.

How to run this program on COSMIC²

Upload either cryoSPARC (.cs) files or RELION STAR files using the ‘Web browser’ upload. After specifying sample symmetry you can then submit the job! Typically it will take 1-3 hours to run for a single particle dataset.

You will see the cryoEF output listed in the STDOUT output file in the COSMIC² gateway.

Example output:

------------------------------------ Output ------------------------------------
Efficiency: 0.80
Mean PSF resolution: 3.39 Å
Standard deviation: 0.34 Å
Worst PSF resolution: 4.06 Å Direction: phi = 45 theta = 61
Best PSF resolution: 2.45 Å Direction: phi = 45 theta = 35
Distribution of PSF resolution: 
2.45 Å - 2.61 Å: 1.89%
2.61 Å - 2.77 Å: 3.66%
2.77 Å - 2.93 Å: 4.95%
2.93 Å - 3.09 Å: 10.85%
3.09 Å - 3.26 Å: 15.21%
3.26 Å - 3.42 Å: 16.27%
3.42 Å - 3.58 Å: 15.57%
3.58 Å - 3.74 Å: 13.68%
3.74 Å - 3.90 Å: 11.67%
3.90 Å - 4.06 Å: 6.25%

------------------------------ Other Output Files ------------------------------
Data for PSF resolution histogram written to file cryosparc_P1_J99_final_particles_PSFres.dat
Fourier space information density written to file cryosparc_P1_J99_final_particles_K.mrc
Real space PSF written to file cryosparc_P1_J99_final_particles_R.mrc

----------------------------- Tilt Recommendations -----------------------------
Recommended tilt angle: 19 deg
Recommended to collect ~1.5 times more particles at this angle than at zero tilt
Recommended tilt angle: 29 deg
Recommended to collect ~2.2 times more particles at this angle than at zero tilt