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SET MP
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; mrc.spi : get defocus using MRC program CTFFIND2
;    
; Requires
;   ctffind*    a shell script
;   readmrc.py    a python script
;
; Inputs:
;        micrographs (in SPIDER format)
;        start, end micrograph numbers
;        parameters to ctffind, including
;                - spherical aberration
;                - electron beam voltage (in kV)
;                - amplitude contrast ratio
;                - magnification
;                - pixel size on scanner (in microns)
;                (see ctffind script for more)
; Outputs:
;       doc file of defocus and astigmatism information.
;       power spectrum generated by ctffind2 (in SPIDER format).
;       text report generated by ctffind2.

; Exclude the edges of the micrograph
x27 = 100  ; X distance from border
x28 = 100  ; Y distance from border

; Parameters for CTFFIND2. Use symbolic vars to send to shell script.

FR G
[cs] 2.26     ; Spherical aberration
FR G
[kv] 300      ; Electron beam voltage in kV
FR G
[ac] 0.1      ; amplitude contrast ratio
FR G
<<<<<<< mrc.spi
[mag] 50000   ; Magnification of original image (final mag on the F30)
=======
[mag] 100000   ; Magnification of original image (final mag on the F30)
>>>>>>> 1.5
FR G
[scansize] 15  ; Pixel size on scanner in microns (7, 14, etc.)

; ----------- Input files --------------

FR G
<<<<<<< mrc.spi
[FILENUMS]filenum1  ; ../all_micrographs     ; file numbers
=======
[FILENUMS]../all_micrographs     ; file numbers
>>>>>>> 1.5
FR G
<<<<<<< mrc.spi
[mic]../Micrographs/mic{****x11}   ; input template for micrographs
=======
[mic]../Micrographs/mic{*****x11}   ; input template for micrographs
>>>>>>> 1.5

; ----------- Output files --------------
FR G
[defocus]new/defocus   ; output doc file
FR G
[mrc_out]new/powmrc   ; output power spectrum template 
FR G
[report]new/report ; output report file, created by CTFFIND2 

; -------------------- END BATCH HEADER -----------------------
x15=[scansize]/[mag]*10000 ; pixel size
;
DE
[defocus]

; temporary files
FR G
[tmp1]tmp89769

FR G
[tmp2]tmp92451.mrc    ; use for MRC power spectrum

FR G
[mrc_mic]tmpmic45.mrc

; column labels for the output file
SD /     micrograph  avg.defocus  defocus1    defocus2       angle  astigmatism
[defocus]
sd e
[defocus]

; get the filenumbers
UD N,x20
[FILENUMS]

DO LB1 x65 = 1,x20

UD x65,x11
[FILENUMS]      ; x11 is now the file number

FI x21,x22
[mic]
(12,2)

x31 = x21 - (2*x27)   ; dimensions
x32 = x22 - (2*x28)

WI
[mic]  ; input
[tmp1]         ; output
(x31,x32)      ; dimensions
(x27,x28)      ; start coords

CP TO CCP4
[tmp1]
[mrc_mic]
<<<<<<< mrc.spi
(32)

(x15,x15,x15) ; pixel size ; let the blank above and below (call default values)
=======
(32)

(x15,x15,x15) ; pixel size ; leave blanks above and below (call default values)
>>>>>>> 1.5

<<<<<<< mrc.spi
;
;
=======
;
VM
echo "calling ctffind with micrograph {****x11}"
;
>>>>>>> 1.5
VM
./ctffind [mrc_mic] [tmp2] [cs] [kv] [ac] [mag] [scansize] > [report]{****x11}

<<<<<<< mrc.spi
CP FROM MRC        ; Comment out these 3 lines if you
[tmp2]             ; don't want to keep the output
[mrc_out]{****x11}  ; power spectrum generated by CTFFIND2.
=======
CP FROM CCP4        ; Comment out these lines if you
[tmp2]              ; don't want to keep the output
[mrc_out]{****x11}  ; power spectrum generated by CTFFIND3.
N
>>>>>>> 1.5

VM
\rm [tmp2]
    
VM
./readmrc.py [report]{****x11} {****x11} >> [defocus].$DATEXT

;VM                      ; Comment out these 2 lines if
;\rm [report]{****x11}    ; you want to keep the report.


LB1

DE
[tmp1]
VM
\rm [mrc_mic]

EN D