; reference-based alignment
; number of particles
x91=1254
; number of reference images
x92=2
; last ring for rotational alignment
x21=35
; first ring for rotational alignment
x22=5
; Search range 
; (the search for translation parameters will be 
; restricted to +/- search range).
x23=6
x24=1


; create the selection document file.
; The image series is consecutive
DOC CREATE
select
1
1-x91

DOC CREATE
selref
1
1-x92


ap mq
ref***
selref
x23,x24
x22,x21
sar****
select
apmq101

;rotate and shift images according to the parameters from AP MQ alignment

do lb3 x55=1,x91
ud ic,x55,x41,x42,x43,x44,x45,x46
apmq101
if(x41.gt.0) then
rt sq
sar{****x46}
ser{****x46}
x43
x44,x45
else
rt sq
sar{****x46}
_1
x43
x44,x45
mr
_1
ser{****x46}
y
lb3
ud ice
apmq101

en d