Tilt Validation in EMAN2

We have implemented Richard Henderson's tilt validation methodology in EMAN2. To do tilt validation you need to:

  1. Collect tilted micrograph pairs. Typically an untilted and tilted micrograph of the same specimen area are collected.
  2. Box out particle pairs. These are images of the same particle but in two different views. To implement this we have developed e2RCTboxer.py, a variant of e2boxer.py, to simultaneously pick pairs pairs from micrograph tilt pairs.
  3. If possible, CTF correct the particle pairs.
  4. Build tilted and untilted stacks of images. The particles in these image stacks must maintain a one-to-one relationship. That is, particle n in the tilted stack must be paerticle n in the untilted stack, but in a different view caused by the tilt geometry.

  5. Determine Euler angles for each particle for each particle pair, using projection matching. Projections are dervied from the 3D model under question. Hence Euler angles wil only be determined correctly if both the 3D model is correct and your 2D image, both untilted and tilted, are of decent quality.
  6. From the Euler angles of the particle pairs, compute the tilt geometry.
  7. In polar format, plot the computed tilt geometries (there will be one tilt geometry for each particle pair). If the tilt geometries form a cluster, and the cluster centers around the experimental tilt geometry, the 3D model is said to be valid. If the cluster's tilt axis is 180 from the correct tilt axis, the 3D model is of the wrong hand, and this can be resolved by simply flipping the hand.

Steps 5-7 are implemented in e2tiltvalidate.py

e2tiltvalidate.py options

Listed below are e2tiltvalidate.py options

Listed below are options specific to making validation plots using e2tiltvalidate.py

Listed below is the option to compute tiltvalidation from a Euler data file rather than from stacks

The file must be of the format:
untilt_image_num, image_name, az, alt, phi
tilt_image_num, image_name, az, alt, phi
For example:
0 untilted 45 45 -50
0 tilted 45 55 -50
1 untilted 20 10 -20
1 tilted 20 0 -20

EMAN2/Programs/e2tiltvalidate.py (last edited 2013-03-27 19:03:46 by StephenMurray)