AP C - Rotation Alignment - classification, unknown references ||

(03/21/12)

PURPOSE

Rotationally aligns an image series with an optional check of its mirrored position and at the same time classifies the images into a specified number of groups.   Example.

SEE ALSO

AP SH [Alignment - multi-reference, exhaustive rotation & shift ||*]
AP REF [Alignment - multi-reference, rotation & shift ||*]
AP SA [Alignment - reference free, Shift ||]
AP SR [Alignment - reference free, Shift & Rotation ||]

USAGE

.OPERATION: AP C

.INPUT FILE TEMPLATE (E.G. PIC****): IMG***
[Give a template for existing image file series to be aligned]

.FILE NUMBERS OR SELECTION DOC. FILE NAME: 1-700
[Enter projection file numbers or the name of the document file containing projection file numbers in the first register.]

.FIRST, LAST RING, & RING SKIP: 5, 15, 1
[Only polar rings with the radii in the range 5-15 (in pixel units) will be analyzed. If skip=0 or 1 then each ring between 5 and 15 will be taken; for skip=2 each second, and so on.]

.ANALYZE FULL OR HALF RING? (F/H): F
[Use 'F' for analyzing complete ring with real data. Use 'H' for analyzing half ring containing autocorrelation function.]

.NORMALIZE UNDER THE MASK? (N/Y): Y
[Use 'Y', for negative stain data to normalize for the negative stain effect.]

.NUMBER OF GROUPS, NUMBER OF ITERATIONS: 5, 30
[Number of groups the images will be divided into and upper limit of iterations permitted (to avoid infinite loop in the case of lack of convergence)]

.CHECK MIRRORED POSITIONS? (N/Y): N
[Optional check of the mirrored images.]

.GROUP SELECTION DOC FILE TEMPLATE: grp***
[Enter template for name of the document files where numbers of images assigned to each group will be placed. One selection doc file will be created for each group.]

.CLASSIFICATION & ALIGNMENT DOC FILE: apca001
[Document file with classification nd rotational alignment results. This is the only output produced by this operation. It contains 4 register columns:

Register    Contents
1    Image file number (May have gaps)
2    Rotation angle
3    Distance from total average (similarity measure), Distance <0 indicates image must be mirrored
4    Classification group number

NOTES

  1. Note that the rotation parameters produced by this operation are given with the proper signs. This means that to rotate the images afterwards, these parameters should be applied directly (without sign reversal). To combine parameters given by repeated alignments, the 'SA P' operation can be used. (Only the angle signs used for 3-D reconstruction from tilted series need to be reversed.)

  2. Usage example: rotkm-ali.spi

  3. Implemented by Paul Penczek. For details see appendix in: P.A.Penczek, J.Zhu, & J.Frank. A common-lines based method for determining orientations for N>3 particle projections simultaneously. Ultramicroscopy, 63, 205-218 (1996).

SUBROUTINES

HALI, NORMAS, ALRQ, FOURING, CROSRNG, UPDTC, ENER, SEEDS, HKMC

CALLER

UTIL4

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