MD
SET MP
0
; SOURCE:  mrc.spi 
;
; PURPOSE: 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
[v27] = 100  ; X distance from border
[v28] = 100  ; Y distance from border

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

[cs] = '2.26'      ; Spherical aberration

[kv] = ' 300'      ; Electron beam voltage in kV

[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

[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{****[v11]}'   ; input template for micrographs
=======
[mic] = '../Micrographs/mic{*****[v11]}'   ; input template for micrographs
>>>>>>> 1.5

; ----------- Output files --------------

[defocus] = 'new/defocus'   ; output doc file

[mrc_out] = 'new/powmrc'   ; output power spectrum template 

[report] = 'new/report' ; output report file, created by CTFFIND2 

; -------------------- END BATCH HEADER -----------------------

MD
SET MP
0

[v15]= [scansize]/[mag]*10000 ; pixel size

DE
[defocus]

; Temporary files
[tmp1]    = 'tmp89769'
[tmp2]    = 'tmp92451.mrc'    ; use for MRC power spectrum
[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 [v20]
[FILENUMS]

DO [v65] = 1,[v20]

   UD [v65],[v11]
   [FILENUMS]      ; [v11] is now the file number

   FI [v21],[v22]
   [mic]
   (12,2)

   [v31] = [v21] - (2*[v27])   ; dimensions
   [v32] = [v22] - (2*[v28])

   WI
   [mic]  ; input
   [tmp1]         ; output
   ([v31],[v32])      ; dimensions
   ([v27],[v28])      ; start coords

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

   ([v15],[v15],[v15]) ; pixel size ; let the blank above and below (call default values)
   =======
   (32)

   ([v15],[v15],[v15]) ; pixel size ; leave blanks above and below (call default values)
   >>>>>>> 1.5

   <<<<<<< mrc.spi
   ;
   ;
   =======
   ;
   VM
   echo "calling ctffind with micrograph {****[v11]}"
   ;
   >>>>>>> 1.5
   VM
   ./ctffind [mrc_mic] [tmp2] [cs] [kv] [ac] [mag] [scansize] > [report]{****[v11]}

   <<<<<<< mrc.spi
   CP FROM MRC        ; Comment out these 3 lines if you
   [tmp2]             ; don't want to keep the output
   [mrc_out]{****[v11]}  ; power spectrum generated by CTFFIND2.
   =======
   CP FROM CCP4        ; Comment out these lines if you
   [tmp2]              ; don't want to keep the output
   [mrc_out]{****[v11]}  ; power spectrum generated by CTFFIND3.
   N
   >>>>>>> 1.5

   VM
   \rm [tmp2]
    
   VM
   ./readmrc.py [report]{****[v11]} {****[v11]} >> [defocus].$DATEXT

   ;VM                      ; Comment out these 2 lines if
   ;\rm [report]{****[v11]}    ; you want to keep the report.


ENDDO

DE
[tmp1]

VM
\rm [mrc_mic]

EN