VO MD - Vector Operation - angular Document file from 'AP MD' output

PURPOSE

Convert output document file from the 'AP MD', 'AP RD', or 'AP RN' operation to an angular document file containing three Eulerian angles. Obsolete, not needed if you use the recommended 'AP SH' instead of the obsolete 'AP MD'

SEE ALSO

VO EA	[Vector Operation - Create Evenly Spaced Angles Document file]
VO RA	[Vector Operation - Rotate Angular document file]
AP MD	[Alignment - Multi reference, rotation ||]
AP SH	[Alignment - multi-reference, exhaustive rotation & shift ||*]

USAGE

.OPERATION: VO MD

.ANGULAR DOCUMENT FILE NAME: REFANG
[Enter the name of the reference angles document file (created by 'VO EA') used to calculate reference projections required for 'AP MD', etc.]

.OUTPUT FROM AP MD/RD/RN DOCUMENT: APMD101
[Enter the name of the document file produced by the 'AP MD' command. This document file should contain 6 columns:

1.Number of the most 2.Distance. 3. "-psi" angle
similar reference Can be used as In-plane rotation
projection. When a similarity measure. angle determined.
this number is negative Output from
the most similar is 'AP MD' document.
a mirrored projection
(see appended SPIDER
procedure). When this
number is zero, the line
is skipped and the output
angular document
file will not contain
corresponding key.


4. Always 0.0 5. Always 0.0 6. Experimental
projection number.

.DOCUMENT: OUTANGLES
[Enter the name for the angular document file that will be produced. This document file will contain three columns with the three Eulerian angles psi, theta, and phi. The key numbers will correspond to experimental projection numbers from column 6 of the 'AP MD', 'AP RD', 'AP RN' output document file. Thus, for image file series with gaps the keys will not be consecutive. Moreover, for the output files from AP RD/RN operations the entries for non-matching projections (marked by 0 in the first column) will be omitted. The angular document file can be subsequently used in the 'BP RP' operation to calculate a refined 3D reconstruction.]

NOTES

1. In 3D space the projection with the direction (psi, theta, phi) has its mirrored [around X-axis] counterpart in the direction:
   (-psi, 180-theta, phi+180).
   To save time, the operation AP MD takes this into account, and each data projection is compared with the reference projection and its mirrored version at the same time. Thus, only half of the total number of reference projections are required, namely, only those with 0<theta<90. If the best match was with the mirrored reference projection, then the number stored in the first column of the document file is equal to the number of the corresponding mirrored reference projection plus an offset equal to the total number of reference projections (see appended SSPIDER proceedure).

2. Implemented by P. Penczek

SUBROUTINES

VOMD

CALLER

DRIV1

The command 'VO MD' is equivalent to the following SPIDER procedure:
;  Prepare ang doc file after the alignment of projections
;
;  APMD101   - Input document file produced by 'AP MD' operation
;  REFANG    - Input document file with 2D reference projections angles 
;              stored in the order (psi, theta, phi)
;  OUTANGLES - Output ang document file to be used for 3D reconstruction

UD N,x88                    ; Find number of images
APMD101

DO LB1 x19=1,x88            ; Loop over all images
   UD IC   x19,x51,x52,x41,x61,x61,x81
   APMD101

   x41=-x41                 ; - the inplane rotation

   IF(x51.EQ.0) GOTO LB1    ; Skip images with no angles determined

   x61=x51
   IF(x51.LT.0)  x61=-x51   ; Index for non-mirrored image

   UD IC,x61,x22,x42,x43    ; Reference angles for this image
   REFANG

   IF(x51.LT.0) THEN        ; Adjust mirrored angles
      x41=x41+180.0         ; Add 180 to inplane rotation
      x42=180.0-x42         ; Adjust theta
      x43=x43+180.0         ; Adjust phi
   ENDIF

   SD x81,x41,x42,x43       ; Save adjusted angles
   OUTANGLES
LB1
EN