Creates align doc file

([grp1],[grp-end],[iter]) ; Creates align doc file
;
; firstalign.pam        ArDean Leith Apr 2003
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; PURPOSE: Copies trans  doc files into initial align doc file
;          (Only used for 'AP MQ' output)
;
; I/O Registers and files are set in: refine settings refine settings.pam.pam); INPUT REGISTERS:
;
; INPUT REGISTERS):
;    [grp1]                        Defocus group set start
;    [grp-end]                        Defocus group set end
;    [iter]                     Iteration in use

FR L
[group_trans]input/trans{**[iter]}_{***[grp]} ; Current group translations doc files

[img1]=1   ; Starting image number
[dum]=0    ; For unused columns

DO LB1 [grp]=[grp1],[grp-end]     ; Loop over defocus group set  
   DE
   [initial_group_align]          ; Next align. doc file

   UD IC [grp],[num-img]          ; Set number of particles in group
   [order_select]                 ; Need this input file

   DO LB2 [img]=[img1],[num-img]    ; Loops over images 

      UD IC [img], [p51],[p52],[p53],[p54] ; Retrieve parameters
      [group_trans]                 ; Translations input doc file 

      ; Save alignment parameters
      [p12]=0
      IF([p54].GT.0) [p12]=-1.0

      ;          <,   <,    <,     REF#, EXP#, INP<, SX,SY,  NPROJ,< DIFF, CCROT
      SD [img], [dum],[dum],[dum], [p12], [img], [p51],[p52],[p53],  [dum],[dum],[dum]
      [initial_group_align]      ; Next align. doc file (output)
   LB2

   UD ICE
   [group_trans]                 ; trans  input doc file

   SD E
   [initial_group_align]         ; Align. param doc file
LB1

RE
;