([n],[phi0],[the0],[psi0],[phid],[thed],[nphi],[nthe],[psin],[mskval],[peaks],[msktype])
; Controls motif search
;
; new_sigs_settings.spi New JAN 2003 Bimal Rath
; Parallelized MAY 2003 ArDean Leith
; Rewritten JUL 2008 ArDean Leith
;
; PURPOSE: Searches for molecular signature (motif) inside search volume.
; Be SURE both volumes have same magnification (1 pixel = "n" nanometer)
; -------------- Edit next 13 input parameters --------------------------
[n]=0 ; Number of OMP processes wanted
; Phi: Starting angle, Ending angle (+ve), & Step size (+ve)
[phi0] = 0
[phin] = 330
[phid] = 30
; Theta: Starting angle, Ending angle (+ve), & Step size (+ve)
[the0] = 0
[then] = 330
[thed] = 30
; Psi: Starting angle, Ending angle (+ve)
; [psid] will be created for uniform sampling of unit sphere
[psi0] = 0
[psin] = 330
; # of peaks to be found, (# of particles expected)
[peaks] = 20 ; 7 actual
; Pixel value for masking (pixels < this value set to: 0, rest set: 1)
[mskval] = .1
; Type of mask to be used.
; NOTE: For globular motifs, rotationally invariant mask can be used.
; Computation will be faster. A cubic motif volume is required.
[msktype] = 1 ; 0 = Rotationally invarient mask, 1 = Asymmetric mask
; --------------------------- INPUT FILE NAMES ----------------------------
; ----------------- May have to edit these names --------------------------
GLO [SEARCH_VOL] = 'input/test_volnc' ; Large volume 384x384x110
; When using a rotationally invariant mask, must use a cubic motif volume
GLO [MOTIF_VOL] = 'input/test_motifnc' ; Volume to be searched for 23x15x15
; When searching a tomographic volume you may need to use a wedge filter on
; the motif to compensate for missing wedge and CTF.
GLO [WEDGE_FILTER] = '*' ; No tomographic wedge filter
; ----------------- OUTPUT FILES ------------------------------------------
; ----------------- No need to edit for default names --------------------
GLO [MOTIF_MASK] = 'work/jnk_mask' ; Motif mask volume (From: 'sigs_pub')
GLO [CUBE_MOTIF_VOL] = 'work/jnk_cube_motif' ; Padded cubic motif (From: 'sigs_pub')
GLO [MOTIF_MASK_FFT] = 'work/jnk_mask_fft_{***[num]}' ; FFT of mask volume (From: 'LO I')
GLO [SEARCH_VOL_FFT] = 'work/jnk_search_fft' ; FFT of search volume (From: 'LO I')
GLO [SEARCH_VOL_SQ_FFT] = 'work/jnk_search_sq_fft' ; FFT of search volume squared (From: 'LO I')
GLO [LSD_VOL] = 'work/jnk_lsd_{***[num]}' ; LSD volume (From: 'LO LSD')
GLO [PEAK] = 'output/jnk_peak_{***[num]}' ; LSD scaled peak volume (From: 'LO')
GLO [SIZES] = 'output/DOC_SIZES' ; Volume sizes
GLO [DOC_FILE_OUT] = 'output/DOC_OUT_{***[num]}' ; Angles and peak search info file stem (From: 'LO')
GLO [DOC_FILE_OUT_T]= 'output/DOC_OUT_***' ; Angles and peak search info file stem (From: 'LO')
GLO [SYNC_DOC_BASE] = 'work/sync_doc' ; Sync. doc file stem for PubSub (From: 'LO')
GLO [PEAK_COMBINED] = 'output/DOC_COMB' ; Combined angles & peak search info file stem
; DIRECTORIES CREATED
GLO [temp_work_dir] = 'work/' ; A scratch dir
GLO [output_dir] = 'output/' ; A shared output dir
; ----------------- END OF OUTPUT FILES -----------------------------------
; AVOID DIVISION BY ZERO
IF ([phid].EQ.0) THEN
[phid] = 1
ENDIF
IF ([thed].EQ.0) THEN
[thed] = 1
ENDIF
[nphi] = INT((([phin]-[phi0])/[phid])+1)
[nthe] = INT((([then]-[the0])/[thed])+1)
RE
;