; Multiplies a reference volume by the CTF & creates ref projections
;
; refproj.bat
;
; PURPOSE: Multiplies a reference volume by the CTF for each defocus group, then
; creates reference projections from each CTFvolume.
;
;Inputs
; ../params ; the parameter doc file
; reference_volume ; reference volume
; radius ; parameter for PJ 3Q (if the value is -1, a default
; value will be computed that is .69 * actual size.)
;
;Outputs
; refangles ; doc file with reference angles
; projlist ; doc file with list of projections
; df***/prj ; template for 2D projections
; df***/refctf ; reference multiplied by CTF
;
; the following values are computed from the params file
;x12 = number of defocus groups
;x72 = electron wavelength (Angstroms)
;x73 = pixel size, Angstroms
;x75 = array dimension, pixels
;
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; I/O PARAMETERS AND FILES ARE SET HERE:
;
; ------------ Parameters ---------------------------------------
x15 = 15 ; delta theta : 15 gives 83 projections
x39 = -1 ; radius : use -1 for default value
; ------------ Input files ---------------------------------------
FR G
[params]../params ; the parameter file
FR G
[refvol]../reference_volume ; input reference volume
FR G
[defocus]../Power_Spectra/order_defgrps ; average defocus group values
; --------------- Output files -------------------------------------
FR G
[refangles]refangles ; output doc file of angles
FR G
[projlist]projlist ; output list of projections
FR G
[df]df{***x22} ; directory template for defocus groups
FR G
[prj]prj**** ; output template for 2D projections
; -------------- END BATCH HEADER ---------------------------------
; delete output document files and get parameters
DE
[refangles]
DE
[projlist]
UD 5,x73 ; pixel size
[params]
x74=0.5/x73 ; max. spatial frequency
UD 6,x71 ; electron energy
[params]
x72 = 12.398 / SQR(x71 * (1022.0 + x71)) ; lambda
UD 7,x79 ; spherical aberration
[params]
UD 8,x61 ; source size
[params]
UD 9,x62 ; defocus spread
[params]
UD 12,x63 ; amplitude contrast ratio
[params]
UD 13,x64 ; Gaussian envelope halfwidth
[params]
UD 17,x75 ; window size
[params]
IF (x39.LT.0) THEN ; get actual size and compute radius
UD 18,x41
[params]
x39 = 0.69 * x41
ENDIF
UD N,x12 ; number of defocus groups
[defocus]
; create the document files
VO EA,x83
x15 ; delta theta
0,0 ; range of theta
0,0 ; range of phi
[refangles] ; output doc file of angles
x83=x83-1
DOC CREATE
[projlist] ; output doc file
1 ; column to be filled
1-x83 ; numbers to put in column
;------------------------------------------
; For each defocus group, multiply the reference volume by the
; appropriate defocus, then use this ctf-reference to generate
; 83 projection images
DO LB1 x21=1,x12
UD x21,x22,x71 ; get defocus group # (x22) and defocus value (x71)
[defocus]
VM
mkdir -p [df]
TF C3
_7 ; output file (complex model CTF)
x79 ; spherical aberration
x71,x72 ; defocus,lambda
x75 ; array dimension
x74 ; maximum spatial frequency
x61,x62 ; source size, defocus spread
(0,0) ; astigmatism, azimuth
x63,x64 ; amplitude contrast ratio, envelope 1/2-width
(-1) ; sign
FT
[refvol]
_2
MU
_2
_7
_4
*
FT
_4
_7 ; output = ctf_multiplied volume
PJ 3Q ; generate projections of a volume
_7 ; input volume
x39 ; radius
[projlist] ; file numbers
[refangles] ; angles doc file
[df]/[prj] ; template for output projection images
LB1
EN
;