AP CM - Alignment - Classification and Alignment

PURPOSE

Rotationally aligns the image series with a check of the mirror position and at the same time classifies the images into 'K' groups.

SEE ALSO

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

USAGE

.OPERATION: AP CM

.ENTER TEMPLATE FOR 2-D IMAGE FILES: UKN***
[Give the name of any of the existing files from the series to be aligned]

.ENTER 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 AND LAST RING: 5,15
[Only rings 5 to 15 will be analyzed]

.SKIP: 1
[If skip=0 or 1, then each ring between 5 and 15 will be taken; for skip=2 every second ring, etc.]

.FULL OR HALF: H
[Full - full ring treated (real data); Half - half ring treated (autocorrelation function).]

.NORMALIZE UNDER THE MASK (Y/N): Y
[For Y, input rings are normalized to compensate 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)]

.OBJECT OUTPUT FILENAME TEMPLATE: obj***
[Enter template for name of the document files where all the objects belonging to the same cluster will be stored.]

.DOCUMENT FILE NAME: apca001
[Document file with classification results. It contains 4 columns:

1.File number 2.Rot. angle 3.Distance 4.Group number
Real number Note that From the Results of
to handle sign of angle total classification
gaps in file should NOT be average.
series. reversed in
formation. of
average.
If the distance (in column #3) is negative,
the image has to be mirrored.]

NOTES

1. Please note that all the parameters produced by this program, namely, rotation and/or shift parameters -- are given with the proper signs. This means that to rotate and/or shift the images afterwards, these parameters should be applied directly (without sign reversal). To combine parameters given by repeated alignments, the 'SA P' command must be used. Only the angle signs used for 3-D reconstruction from tilted series need to be reversed.

2. 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 (1996) 205-218.

SUBROUTINES

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

CALLER

UTIL4

Example of the SPIDER procedure using 'AP CM'.

; b22.apc
; Rotate particles and calculate group averages

; number of particles
X92=338

; number of groups
X91=3

AP CA
rts/pur***
1-x92
5,14
0
F
Y
X91,50
clas/select***
clas/apca001

DO LB1 I=1,X92
   UD IC,X0,X21,X22,X23,X24
   clas/apca001

   ; Rotate and mirror particles
   ; rts/pur - input image series, rts/apc - rotated images
   IF (X23.GT.0.0)  THEN
      RT SQ
      rts/pur{***X21}
      rts/apc{***X21}
      X22
      (0,0)
   ELSE
      RT SQ
      rts/pur{***X21}
      _1
      X22
      (0,0)

      MR
      _1
      rts/apc{***X21}
      Y
   ENDIF
LB1

; Calculate the average for each goup (only if there are more than 2 particles)

DO LB4 X71=1,X91
   ; Check whether the file exists
   IQ FI,X72
   clas/select{***X71}

   IF(X72.EQ.0.0) GOTO LB4

   ; Get number of images in this group
   UD N,X72
   clas/select{***X71}
   IF(X72.LE.2) GOTO LB4

   AS DC
   rts/apc***
   clas/select{***X71}
   A
   clas/avg{***X71}
   clas/var{***X71}
LB4

EN