; Apply CTF correction
;
; SOURCE: ctf.spi
;
; PURPOSE: Apply CTF correction to all the defocus group odd/even volumes,
; then compute the FSC resolution curve for the combined data set.
;
; This batch file produces the initial volume, vol001, which is
; copied to the Refinement/input directory.
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
; ----------------- I/O PARAMETERS --------------------------------
x73 = 3 ; SNR for CTF correction (TF CTS)
; -------------------- Input files -----------------------------------
FR G
[params]../params ; Parameter file
FR G
[defgrps]sel_group_cclim ; Selection file for defocus groups
FR G
[voleven]vol001_even ; "even" volumes
FR G
[volodd]vol001_odd ; "odd" volumes
; -------------------------- Output files ---------------------------
FR G
[ctf]ctf/ctf ; Ctf file stem
FR G
[res]combires ; Resolution curve for combined output
FR G
[vol]vol001 ; CTF-corrected volume of combined data set
FR G
[volcopy]../Refinement/input/vol01 ; Copy of volume used for refinement
; -------------- END BATCH HEADER ------------------------------
MD
SET MP
0 ; Use all processors available
VM ; Make the ctf output directory
mkdir -p ctf
VM ; Make the Refinement directory
mkdir -p ../Refinement
VM ; Make the Refinement/input directory
mkdir -p ../Refinement/input
FR G
[tmp]tmpres88 ; Temp. file (deleted)
DE
[res]
; Get parameters
UD 5,x41 ; Pixel size
[params]
UD 6,[kv] ; KV
[params]
UD 7,[cs] ; Cs
[params]
UD 8,[ss] ; Source size
[params]
UD 9,[defspr] ; Defocus spread
[params]
UD 12,[acr] ; ACR
[params]
UD 13,[genv] ; Gaussian envelope
[params]
UD 17,[winsiz] ; Window size
[params]
[lambda] = 12.398 / SQR([kv] * (1022.0 + [kv])) ; Lambda
[maxspf] = 1.0 / (2.0 * x41) ; Max. spatial. freq.
; Create CTF file for each defocus group
UD N,[numgrps] ; Find number of defocus groups
[defgrps] ; (input)
DO LB1 [numgrp] = 1,[numgrps] ; Loop over all defocus groups
UD [numgrp],[grp],[numparts],[def] ; Get current group number
[defgrps] ; Group selection file (input)
TF C3 ; Create a model CTF (3D, complex)
[ctf]{***[grp]} ; Output file (output)
[cs] ; Cs
[def],[lambda] ; Defocus, lambda
[winsiz] ; Dimension of volume
[maxspf] ; Max. spatial freq.
[ss],[defspr] ; Source size, defocus spread
(0,0) ; Astigmatism, azimuth
[acr],[genv] ; Amplitude contrast ratio, Gaussian halfwidth
(-1) ; Sign
LB1
; The 'TF CTS' command works on all defocus groups at once
TF CTS ; CTF correction
df***/[voleven] ; Template for image file (input)
[defgrps] ; Group selection file (input)
[ctf]*** ; Template for ctf file (input)
x73 ; SNR
_1 ; Temp. inline file (output)
TF CTS
df***/[volodd] ; Template for image file (input)
[defgrps] ; Group selection file (input)
[ctf]*** ; Template for ctf file (input)
x73 ; SNR
_2 ; Temp. inline file (output)
; Add the odd and even volumes together to make combined volume
AD
_1
_2
[vol] ; Volume (output)
*
; Compute the combined resolution curve
DE
[tmp]
RF 3 ; Compute resolution curve
_1 ; First input volume
_2 ; Second input volume
(0.5) ; Ring width
(0.2,2.0) ; Lower, upper scale factors
C ; C = missing cone
(90.0) ; Max. tilt angle
(3) ; Factor for noise comparison
[tmp] ; Output doc file (output)
DOC REN ; Renumber the doc file
[tmp]
[tmp] ; Doc file (output)
UD N,[nline] ; Determine number of lines in doc file
[tmp] ; Doc file (input)
SD / NORM'D FREQ DPR FSC FSCCRIT VOXELS
[res] ; Doc file (output)
DO LB2 [line] = 1,[nline]
UD [line], [v62],[v63],[v64],[v65],[v66]
[tmp] ; Doc file (input)
SD [line], [v62],[v63],[v64],[v65],[v66]
[res] ; Doc file (output)
LB2
DE
[tmp]
CP ; Copy initial volume to refinement dir
[vol] ; Volume (output)
[volcopy] ; Volume (output)
VM
echo ' 'Created CTF-corrected volume of combined data set: [vol]
VM
echo ' '
EN
;