(x91,x31,x44,x92,x79,x27)                                      
FR
?converted micrograph image?[conv-micrograph]
; micx55
                                          
FR
?the doc file of micrograph image?[docfile]
; ndcx55

FR
?auto selected paticles?[selected] 
;win/ser******

FR
?doc file with corrected upperleft corner coord for particles?[ulcoord]
; sndcx55

x99=0 

; Column labels for the sndc file
SD /     x-coord     y-coord    particle #
[ulcoord]
                                                                 
FI x23,x24                                                                      
[conv-micrograph]                                              
(12,2)   

x73=INT(x92/2)

x63=INT(x92/x44)+1 
                   
; Decimate by x44                                                                    
DC S
[conv-micrograph]                                                                          
_5                                                                              
x44,x44                                                                         

CE
_5
_6
L
G
(30,30)                                                                                                         
DE
_5

FQ NP                                                                           
_6                                
_4                                                                              
(3)                                                                             
x31                                                                                                                                                         

; Filter radius ~ (particle size/2)+1)/interpolated x dimension                  
AT PK                                                                           
_4                                                                              
x79                                                                             
(0.75)                                                                          
x63,x63                                                                         
[docfile]
                                                                      
DE                                                                              
_4                                                                              
;1/x44 of particle size and window size                                         

UD -1,x81                                                                       
[docfile] 
                                                                   
MS                                                                              
_6@                                                                             
x92,x92,1                                                                     
x81
                                                                             
;---------------------------------------                                        
IF(x81.EQ.0) GOTO LB1                                                           

SD E                                                                            
[docfile]                                                                     

DO LB2 x77=1,x81                                                                  
   UD IC,x77,x21,x22                                                               
   [docfile]                                                                      
   x21=x21*x44-x73                                                                 
   x22=x22*x44-x73                                                                 
   ; Subtract half particle size                                                    

   WI                                                                              
   [conv-micrograph]                                                                          
   _9                                                                              
   x92,x92                                                                         
   x21,x22 
                                                                        
   ; Window size is particle size                                                   
   x99=x99+1                                                                       
   RA                                                                              
   _9                                                                              
   _2                                                                              

   CE FIT                                                                          
   _7                                                                              
   _2                                                                              
   _8                                                                              
   _6@{******x99}                                                                         

   ; Selected particles are put in stack for alignment                             
LB2                                                                             

DO LB4 x41 = 1, x81                                                               
   CP
   _6@{******x41}
   _2

   x21=0
   x22=0
   DO LB21 x81=1,100
      SH
      _2
      _5
      -x21,-x22

      RO I
      _5
      _4

      CC N
      _5
      _4
      _3

      PK x11,x12
      _3
      (1,0)
      IF(x11.NE.0.0) GOTO LB41
      IF(x12.EQ.0.0) GOTO LB31
      LB41
      x21=x21+x11
      x22=x22+x12
   LB21
LB31

IF(x21.GT.x27) THEN
   x21=0
   x22=0
ENDIF
IF(x22.GT.x27) THEN
   x21=0
   x22=0
ENDIF

UD IC,x41, x48, x49                                                             
[docfile]
x61 = x48*x44 - x73 + x21                                                    
x62 = x49*x44 - x73 + x22 
                                                                         
x91 = x91 + 1 

SD x41, x61, x62, x91    
[ulcoord]                                                                    
         
WI                                                                              
[conv-micrograph]                                                                          
_9                                                                              
x92,x92                                                                         
x61,x62
                                                                   
RA                                                                              
_9                                                                              
_2  
                                                                            
CE FIT                                                                          
_7                                                                              
_2                                                                              
_8                                                                              
[selected]x91 
                                                                   
LB4   
                                                                          
DE                                                                              
_6                                                                              
UD ICE                                                                          
[docfile]
SD E
[ulcoord]                                                                      
DE                                                                              
[conv-micrograph]                                                                         
LB1                                                                             
RE