AP RNS - Alignment - multi-reference, rotation, no mirror check ||

PURPOSE

Compares a single experimental image with a series of reference images. Finds the in-plane Euler rotation which aligns the experimental image with the most-similar reference image. Mirrored positions are NOT checked.
(See align_overview.html for comparison of 'AP' operations.)

SEE ALSO

VO EA	[Vector Operation - Create Doc File Containing Evenly Spaced Angles]
VO MD	[Vector Operation - angular Document file from 'AP MD' output]
VO RAS	[Vector Operation - Rotate Angular doc file & Set angle]
AP RN	[Alignment - multi-reference, restricted projections, no mirror check ||]
AP C	[Rotation Alignment - classification, unknown references ||]
AP MD	[Alignment - Multi reference, rotation ||]
AP RA	[Alignment - Reference free, Rotation ||]
AP RD	[Alignment - multireference, restricted projections ||]
AP SA	[Alignment - reference free, Shift ||]
AP SR	[Alignment - reference free, Shift & Rotation ||]

USAGE

.OPERATION: AP RNS [num],[cc],[psi]

.TEMPLATE FOR REFERENCE IMAGE SERIES: REF***
[Give the template name of the existing file series of reference images (typically projections).]

.FILE NUMBERS OR SELECTION DOC. FILE NAME: SELECTREF
[Enter numbers of reference files. The file numbers can also be read from a selection document file where file numbers are contained in the first register (not the keys).]

.FIRST, LAST RING & SKIP: 5,15,1
[Only rings with radii in the range 5-15 will be analyzed. [If skip=0 or 1, then every ring between 5 and 15 will be taken; for skip=2, every second ring; etc.]

.REFERENCE-RINGS FILE: REF001
[Give name of reference-rings file. If the file exists, SPIDER will read the reference-rings data from this file and will not read the reference image file series. If this file does not exist, SPIDER will create/store the reference-rings data in incore memory. If SPIDER is unable to allocate sufficient memory for the reference-rings data then the reference-rings file must exist. In that case, use operation 'AP I' to create the reference-rings file. More than one SPIDER run can use the same reference-rings file.
Note that old responses 'W', 'Y', & 'N' are now obsolete.

.IMAGE: TEST
[Give the name of the existing experimental image. This image will be checked for alignment versus the reference images.]

The registers receive the output.

Reg 1. Number of the most similar reference projection.

Reg 2. Not-normalized correlation coefficient.
Can be used as a similarity measure.

Reg 3. "-psi" angle.
In-plane rotation angle determined. To use in 3D reconstruction programs invert the sign.

NOTES

1. The reference projections (of the existing structure) can be created using 'VO EA' and 'PJ 3Q' operations. 'VO EA' creates an angular document file with quasi-evenly spaced projection directions and 'PJ 3Q' creates projections of the volume according to this doc file.

2. The operation switches automatically between in-core and on-disk versions depending on the memory available. The reference rings file can be used in either case.

3. The operation is computationally intensive. The code is parallel.

4. An example of the SPIDER batch program which can be used to produce an angular document file from the output document file of this operation is included in the manual chapter for the operation 'VO MD'.

5. Implemented by: Paul Penczek & ArDean leith

SUBROUTINES

NORMAS, ALRQS, ALPRBS, CROSRNG_DS, FRNGS, PRB1D, FFTR_D, FFTC_D, APPLYW

CALLER

UTIL4