Centilt

align_tilt_pairs

Purpose

This utility allows you to center the tilted images of all tilted-untilted image pairs. Besides, the in-plane rotation of the untilted imagesPsi, is copied to the first-rotationPhi of the tilted ones. Therefore, the untilted images should be aligned (using the align2d program), prior to applying centilt.

The centering of the tilted images is based on cross-correlation with the untilted images. The-max_shift option is a valuable tool to discard bad images. Too many discarded images may indicate problems:

• If the particles under study are disc-shaped and lying flat on the micrograph (i.e. the have a relatively low height (Z) and are more-or-less spherically shaped inXY), centilt is expected to give good results using the default options.
• If the particles have a different shape, the centering may be poor, since especially in theX direction the shift becomes poorly defined. In these cases, three alternative options may be tried:
  • -skip_stretching will skip the cosine-stretching prior to centering
  • -force_x_zero will force the shift in theX direction to be zero, and will only center the images in theY direction
  • -skip_centering will skip the entire centering, so that only thePsi angle of the tilted images will be modified.

Usage

$ align_tilt_pairs ...

Parameters

• `` Input selfile with untilted images
• `` Input selfile with tilted images. (Untilted and tilted selfile should have same number of entries, and the same order is assumed for image pairs)
• `` Extension for output images ([filename].[extension]) and output selfile (`[rootname]_[extension].sel`). If none is provided input images and selfile will be overwritten
• `` Write document file with rotations, translations and correlation coefficients. Recommended)
• `` Discard images which shift more (in pixels)
• `` Default action is to stretch the tilted images inX direction by`1/cos(tilt_angle)`, before centering them. Use this option to skip it
• `` Force x-shift to be zero
• `` Default action is to center tilted images based on cross-correlation with the untilted pairs. Use this option to skip it

Examples and Notes

Typical use of this program:

$ align_tilt_pairs -u g0u.sel -t g0t.sel -doc centilt.doc -max_shift 10 -oext cen

The input images and selfile are not overwritten, instead new images calledimagename.cen are written out, with a corresponding selfile calledg0t_cen.sel. This selfile could be used in a subsequent volume reconstruction using ART. Any image that would shift more than 10 pixels will be discarded, i.e. it will not be included in the output selfile, and no.cen image is written out.

It is always a good idea to output document files likecentilt.doc, since it allows to restore the angles and shifts from a previous point in the image processing pathway, using the program headerinfo.

--Main.AlfredoSolano - 22 Jan 2007