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make_frealign_param_APPION.spi
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make_frealign_param_APPION.spi
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; b20_get_sel_angles_sel_shifts_final.spi
;
;
; This batch gets sel_angles and sel_shifts_final and puts them in 1 doc file in
; preparation for frealign.
;
;;;;;;;;;;;;;;;;
FR
?Appion ctf param file? <appion>
FR
?Input shifts file? [shifts]
FR
?Input angular file? [angular]
RR x71
?Magnification?
UD N x12
<appion>
;;;;;;;;;;;;;;;;
;x12=13988 ;#of particles
;x13=4 ;round of refinement # (directory #)
x19=360
x20=180
x21=-1
x70=0.0
; magnification
;x71=65789.
DO LB1 x11=1,x12
;
; Get angular file
;
UD IC,x11,x14,x15,x16
[angular]
;x14=x19-x14 ;make psi negative
;x16=x19-x16 ;make phi negative
;
; Get shifts
;
UD IC,x11,x17,x18
[shifts]
;x17=2*x17 ;multiply x shift by 2 to account for decimation factor
;x18=2*x18 ;multiply y shift by 2 to account for decimation factor
;x17=x17*4.56
;x18=x18*4.56
if(x14.LT.0.0)x14=x14+360.
if(x14.LT.0.0)x14=x14+360.
if(x14.GT.360.0)x14=x14-360.
if(x14.GT.360.0)x14=x14-360.
SD x11,x14,x15,x16,x17,x18
angles_and_shifts
;
; get ctf parameters, add mag. and "phase residuals"
;
UD IC,x11,x89,x88,x87,x86,x85,x84,x21,x22,x23,x24
<appion>
sd x71,x21,x22,x23,x24,x70,x70
ctf_param
LB1
SD E
angles_and_shifts
UD ICE
[angular]
UD ICE
[shifts]
UD ICE
<appion>
sd e
ctf_param
;
; Format the parameters for frealign.
;
VM
fre_format_param.sh angles_and_shifts.spi ctf_param.spi parameters_in_01.spi
VM
rm -f angles_and_shifts.spi ctf_param.spi
EN D