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Listed below are e2tiltvalidate.py options
 * untiltdata, options specifies the untilted particles stack
 * tilteddata, option specifies the tilted particles stack
 * volume, option specifies the volume to validate. The volume needs to be of the same dimensions, as the stacks and the mag(apix) need to be of same scale.
 * maxtiltangle, option specifies the maximum acceptable computed tilt angle. Any tilt angles above this value are rejected and not considered for further processing/plotting.
 * quaternion, when this option is specified, the tilt angle and tilt axis are computed using quaternion mathematics, other wise Euler angles are utilized.
 * sym, option to specify the symmetry of the 3D volume. Note that the 3D model should be aligned to the tilt axis before symmetry can be utilized. To align a volume to the tilt axis, use e2sysmsearch.py
 * docontourplot, when this option is specified, a validation contour plot is computed. For more information see: http://www.ncbi.nlm.nih.gov/pubmed/14568533

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

  • untiltdata, options specifies the untilted particles stack
  • tilteddata, option specifies the tilted particles stack
  • volume, option specifies the volume to validate. The volume needs to be of the same dimensions, as the stacks and the mag(apix) need to be of same scale.
  • maxtiltangle, option specifies the maximum acceptable computed tilt angle. Any tilt angles above this value are rejected and not considered for further processing/plotting.
  • quaternion, when this option is specified, the tilt angle and tilt axis are computed using quaternion mathematics, other wise Euler angles are utilized.
  • sym, option to specify the symmetry of the 3D volume. Note that the 3D model should be aligned to the tilt axis before symmetry can be utilized. To align a volume to the tilt axis, use e2sysmsearch.py
  • docontourplot, when this option is specified, a validation contour plot is computed. For more information see: http://www.ncbi.nlm.nih.gov/pubmed/14568533

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