([n],[phi0],[the0],[psi0],[phid],[thed],[psid],[nphi],[nthe],[npsi],[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] = 0; [phin] = 350
[phid] = 350
; Theta: Starting angle, Ending angle (+ve), & Step size (+ve)
[the0] = 0
[then] = 0 ;[then] = 180
[thed] = 10
; Psi: Starting angle, Ending angle (+ve), & Step size (+ve)
; [psid] will be modified be 1/sin([theta]) for uniform sampling of unit sphere
[psi0] = 0
[psin] = 330
[psid] = 30
; # of peaks to be found, (# of particles expected)
[peaks] = 10
; 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] = 0 ; 0 = Rotationally invarient mask, 1 = Asymmetric mask
; --------------------------- INPUT FILE NAMES ----------------------------
; ----------------- May have to edit these names --------------------------
FR G
[SEARCH_VOL]input/jnk_test_vol ; Search volume 384x384x110
; When using a rotationally invariant mask, must use a cubic motif volume
FR G
[MOTIF_VOL]input/jnk_test_motif ; Volume to be searched for 20x20x20
; Use the mask that was used to separate a volume eg. 40s masked from 80s
; If "TH M" was used for the purpose, you may need to use "DI" to dilate
; the mask a little bit and use the dilated mask here.
FR G
[MASK_PKR]input/dum_mask ; Peak restricting mask UNUSED !!!!!!!
; When searching a tomographic volume you may need to use a wedge filter on
; the motif to compensate for missing wedge and CTF.
FR G
[WEDGE_FILTER]* ; No tomographic wedge filter
;
; ----------------- OUTPUT FILES ------------------------------------------
; ----------------- No need to edit for default names --------------------
FR G
[MOTIF_MASK]work/jnk_mask ; Motif mask volume (From: 'sigs_pub')
FR G
[CUBE_MOTIF_VOL]work/jnk_cube_motif ; Padded cubic motif (From: 'sigs_pub')
FR G
[MOTIF_MASK_FFT]work/jnk_mask_fft ; FFT of mask volume (From: 'LO I')
FR G
[SEARCH_VOL_FFT]work/jnk_search_fft ; FFT of search volume (From: 'LO I')
FR G
[SEARCH_VOL_SQ_FFT]work/jnk_search_sq_fft ; FFT of search volume squared (From: 'LO I')
FR G
[LSD_VOL]work/jnk_lsd ; LSD volume (From: 'LO LSD')
FR G
[PEAK]output/jnk_peak ; LSD scaled peak volume (From: 'LO')
FR G
[DOC_FILE_OUT]output/DOC_OUT ; Angles and peak search info file stem (From: 'LO')
FR G
[sync_doc]work/sync_doc ; Sync. doc file stem for PubSub (From: 'LO')
FR G
[PEAK_COMBINED]output/DOC_COMB ; Combined angles & peak search info file stem
; DIRECTORIES CREATED
FR G
[temp_local_dir]local/ ; A local scratch dir (From: 'sigs_pub')
FR G
[temp_work_dir]work/ ; A scratch dir (From: 'sigs_pub')
FR G
[output_dir]output/ ; An output dir (From: 'sigs_pub')
; ----------------- END OF OUTPUT FILES -----------------------------------
; AVOID DIVISION BY ZERO
IF ([phid].EQ.0) THEN
[phid] = 1
ENDIF
IF ([thed].EQ.0) THEN
[thed] = 1
ENDIF
IF ([psid].EQ.0) THEN
[psid] = 1
ENDIF
[nphi] = INT((([phin]-[phi0])/[phid])+1)
[nthe] = INT((([then]-[the0])/[thed])+1)
[npsi] = INT((([psin]-[psi0])/[psid])+1)
RE
;