AP RN - Alignment - multi-reference, restricted projections, no mirror check ||

(1/28/04)

PURPOSE

Compares a set of experimental images with a set of reference images. For each experimental image, it finds the in-plane Euler rotation which aligns the experimental image with the most-similar reference image. An experimental image is only compared with reference images within a restricted angular range. Mirrored positions are NOT checked. The only difference between this operation and 'AP RD' is how they handle mirroring.
(See align_overview.html for comparison of 'AP' operations.)
OBSOLETE! USE 'AP REF' INSTEAD!

SEE ALSO

AP RA [Alignment - Reference free, Rotation ||]
AP RD [Alignment - multireference, restricted projections ||]
AP REF [Alignment - multi-reference, rotation & shift ||*]

USAGE

.OPERATION: AP RN
<or>
AP RN X10,X11,X12,X13,X14,X15,X16

.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 IMAGE ANGLES DOCUMENT FILE: REFANGLES
[Enter the name of the angular document file containing Eulerian angles of reference images (projections): psi, theta, phi.]

.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.

.TEMPLATE FOR IMAGE SERIES TO BE ALIGNED: DAT***
[Give the template name of the existing file series of experimental images. These images will be checked for alignment versus the reference images.]

.FILE NUMBERS OR SELECTION DOC. FILE NAME:1-21
[Enter numbers of experimental image 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).]

.EXPERIMENTAL IMAGES ANGLES DOCUMENT FILE: angles001
[Enter the name of the angular document file containing Eulerian angles of experimental images (projections: psi, theta, phi. Experimental images will be compared with only these reference images whose normal is within a specified range from this angular value.]

.RANGE OF ANGULAR SEARCH FOR PROJECTIONS: 20.0
[Experimental images will be compared with only these reference images whose normal is within 20 degrees range.]

If registers were specified on the operation line then no output document file is created. Instead the registers receive the output that normally would be put into the document file. This is useful when only a single image is being aligned.

.OUTPUT ANGLES DOCUMENT FILE: APMD101
[This is the only output produced by this program. It contains 7 register columns:

1. Number of the most similar reference projection.
When no matching projection was found within the angular range specified, this column will contain 0.

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

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

4. Always 0.0

5. Always 0.0

6. Experimental image number.

7. Angular change for projection.]

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 output document file created by 'AP MD' can be converted to the angular document file using 'VO MD' operation. Please note that in this case the angular document file created by 'VO EA' is required.

  3. The operation switches automatically between in-core and on-disk versions depending on the memory available. The scratch.file is created/required in either case.

  4. 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.

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

  6. 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'.

  7. Implemented by: Paul Penczek

SUBROUTINES

APMASTER, APRINGS, NORMAS, ALRQS, ALPRBS, CROSRNG_MS, FRNGS, PRB1D, FFTR_D, FFTC_D, APPLYW

CALLER

UTIL4
The following example procedure demonstrates how to apply parameters found 
(in-plane rotation) to the input images:

; x91 - number of images
x91=500
DO LB1 x21=1,x91
   UD IC,x21,x51,x52,x53,x61,x61,x81
   apmd500
   IF(x51.EQ.0) THEN
      CP
      avs{***x81}
      avt{***x81}
   ELSE
      RT SQ
      avs{***x81}
      avt{***x81}
      x53
      (0,0)
      SD x21,x51,x52,x53
      apmdcnv
   ENDIF
LB1 
SD E
apmdcnv
EN

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