; Multiplies reference volume by the CTF & creates ref projections
;
; SOURCE: refproj.spi
;
; PURPOSE: Creates reference projections from a reference volume.
; If desired, separate references can be created for each
; defocus group. In that case, the reference volume is first
; multiplied by the CTF for each defocus group
; (Set [usectf] = 1).
;
; If [usectf] = 0, then a single set of reference projections
; is created, with no modification by the CTF.
;
; The following values are retrieved from the params file
; [numgrp] = Number of defocus groups
; [pix_size] = Pixel size, Angstroms
; [pixels] = Array dimension, pixels
; [ee] = Electron energy
; [spab] = Spherical aberration
; [ss] = Source size
; [defspr] = Defocus spread
; [acr] = Amplitude contrast ratio
; [geh] = Gaussian envelope halfwidth
;
; ------------ Parameters ---------------------------------------
[dtheta] = 15 ; Delta theta: 15 gives 83 projections
[radius] = -1 ; Radius: use -1 for default value
[usectf] = 1 ; Multiply references by CTF (0= Do not, use non-CTF references)
; ------------ Input files ---------------------------------------
FR G
[params]../params ; The parameter doc. file
FR G
[refvol]../reference_volume ; Reference volume
FR G
[defocus]../Power_Spectra/order_defgrps ; Defocus group doc. file
; --------------- Output files -------------------------------------
FR G
[refangles]refangles ; Doc file of projection angles
FR G
[proj_dir]projs ; Dir for projection stacks
FR G
[prj][proj_dir]/prj_ ; Template for 2D projections (stack files)
FR G
[usectf_file]ctf_refs ; Signal File indicates refs are multiplied by CTF
; -------------- END BATCH HEADER ---------------------------------
MD
TR OFF ; Decrease results file output
MD
VB OFF ; Decrease results file output
MD
SET MP
0 ; 0 = use all processors available
VM
mkdir -p [proj_dir]
; Delete output document files and get parameters
DE
[refangles]
DE
[usectf_file]
IF ([radius].LT.0) THEN ; Get actual size and compute radius
UD 18,[size]
[params]
[radius] = 0.69 * [size]
ENDIF
IF ([usectf].GT.0) THEN
; Set "flag" file for 'AP SH'. If this file exists, use CTF-multiplied refs
SD 1,[usectf]
[usectf_file]
UD 5,[pix_size] ; Pixel size
[params]
[spfreq]=0.5/[pix_size] ; Max. spatial frequency
UD 6,[ee] ; Electron energy
[params]
[lambda] = 12.398 / SQR([ee] * (1022.0 + [ee])) ; Lambda
UD 7,[spab] ; Spherical aberration
[params]
UD 8,[ss] ; Source size
[params]
UD 9,[defspr] ; Defocus spread
[params]
UD 12,[acr] ; Amplitude contrast ratio
[params]
UD 13,[geh] ; Gaussian envelope halfwidth
[params]
UD 17,[pixels] ; Window size
[params]
UD N [numgrp] ; Number of defocus groups
[defocus]
ENDIF
; Create the angles document files
VO EA [numang]
[dtheta] ; Delta theta
0,0 ; Range of theta
0,0 ; Range of phi
[refangles] ; Output doc file of angles
[numang] = [numang] - 1
;------------------------------------------
; For each defocus group, multiply the reference volume by the
; appropriate defocus, then use this ctf-reference to generate
; 83 projection images
IF ([usectf].GT.0) THEN
; CTF correction
FT ; Fourier transform
[refvol] ; Reference volume (input)
_2 ; Fourier of reference volume (output)
DO LB1 [iter]=1,[numgrp] ; Loop over all defocus groups
UD [iter], [grp],[def] ; Get defocus group & defocus value
[defocus]
TF C3 ; Transfer Function - Complex 3D
_7 ; Complex model CTF (output)
[spab] ; Spherical aberration
[def],[lambda] ; Defocus, lambda
[pixels] ; Array dimension
[spfreq] ; Maximum spatial frequency
[ss],[defspr] ; Source size, defocus spread
(0,0) ; Astigmatism, azimuth
[acr],[geh] ; Amplitude contrast ratio, envelope 1/2-width
(-1) ; Sign
MU ; Multiply
_2 ; Fourier transform of ref. volume (input)
_7 ; Complex model CTF (input)
_4 ; CTF multiplied Fourier volume (output)
*
FT ; Reverse Fourier transform
_4 ; CTF multiplied Fourier volume (input)
_7 ; CTF_multiplied volume (output)
VM
echo ' 'Group: {***[grp]} Created: {***[numang]} CTF corrected projections
; Projection
PJ 3Q ; Generate projections of a volume
_7 ; Volume to be projected (input)
[radius] ; Radius
(1-[numang]) ; List of file numbers
[refangles] ; Angles doc file (input)
[prj]{***[grp]}@**** ; Template for projection stack (output)
LB1
ELSE
; No CTF correction i.e. single defocus group
[grp]=1 ; Group number
VM
echo ' 'Creating: {***[numang]} reference projections
; Projection
PJ 3Q ; Generate projections of the volume
[refvol] ; Volume to be projected (input)
[radius] ; Radius
(1-[numang]) ; List of file numbers
[refangles] ; Angles doc file (input)
[prj]{***[grp]}@**** ; Template for projection stack (output)
ENDIF
VM
echo ' '
EN
;