; mrc.bat : 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

x77 = 1   ; start micrograph
x78 = 1   ; end micrograph

; Parameters for CTFFIND2

FR G
<cs> 2.00     ; Spherical aberration
FR G
<kv> 200      ; Electron beam voltage in kV
FR G
<ac> 0.1      ; amplitude contrast ratio
FR G
<mag> 50000   ; Magnification of original image
FR G
<scansize> 14  ; Pixel size on scanner in microns (7, 14, etc.)


FR G
<mic>../Micrographs/mic    ; input template for micrographs

FR G
<defocus>defocus   ; output doc file

FR G
<mrc_out>pow   ; output power spectrum template 

FR G
<report>report ; output report file, created by CTFFIND2 

; -------------------------------------------

FR G
<tmp1>tmp89769

FR G
<tmp2>tmp92451.mrc    ; use for MRC power spectrum

FR G
<mrc_mic>tmp12345.mrc


DO LB1 x11 = x77,x78

FI x21,x22
<mic>{***x11}
(12,2)

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

WI
<mic>{***x11}  ; input
<tmp1>         ; output
(x31,x32)      ; dimensions
(x27,x28)      ; start coords

CP TO MRC
<tmp1>
<mrc_mic>
(-9999)

VM
ctffind <mrc_mic> <tmp2> <cs> <kv> <ac> <mag> <scansize> > <report>{***x11}

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.

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