([sp_pixsiz],[r2],[alignsh],[prj-radius],[iter1],[iter-end],[sp_lambda],[small-ang],[sp_winsiz])
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; Sets refinement parameters and files
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; SOURCE: spider/docs/techs/recon/newprogs/refine_settings.pam
; New ArDean Leith Jul 2002
; [] ArDean Leith Dec 2005
; Rewritten More stacks ArDean Leith Dec 2006
; Input locations altered ArDean Leith Dec 2009
; Variable assignment ArDean Leith Jan 2010
; Uses 'AP SH' for 2 iters ArDean Leith Oct 2010
; Even-odd replaced ArDean Leith Jan 2011
; Dala removal ArDean Leith Jan 2012
; [pixsiz] returned, fsc, ofsc... ArDean Leith Aug 2012
; Skip 3.3,3... ArDean Leith Sep 2012
; [ang-steps] changed for 'AP SH' use ArDean Leith Apr 2015
; [converg] removed ArDean Leith Apr 2015
;
; INPUT REGISTERS:
; none
;
; OUTPUT REGISTERS (SET BELOW):
; [sp_pixsiz] Pixel size (A)
; [r2] Object alignment radius (pixels)
; [alignsh] Alignment shift +- allowed (pixels)
; [prj-radius] Object projection radius (pixels)
; [iter1] Starting iteration
; [iter-end] Ending iteration
; [sp_lambda] Electron wavength Lambda (A)
; [small-ang] Small angle refinement flag (1 = true)
; [sp_winsiz] Image/window size = volume size
;
; ============== DO NOT COPY FROM WEB BROWSER ==============
;
; ---- Adjust these parameters for your project -------------------- EDIT -----
[alignsh] = 6 ; Alignment shift (pixels) searched is +- this value
[iter1] = 1 ; Starting alignment step (iteration)
[iter-end] = 8 ; Ending alignment step (iteration)
[diam] = 349 ; Diameter of the structure (A) used in alignment search.
; Diameter is used to find radius for last alignment ring.
; This default is for a ribosome. EDIT as needed!
[win-frac] = 0.95 ; Fraction of window diameter used in projection (.95 = use 95% of window size)
[small-ang] = 1 ; Use small angle refinement instead of regular (1 == Yes)
; Following two variables are used during refinement (one value / iteration) (Defined for: 20 iterations)
IF ( [small-ang] .NE. 1 ) THEN
; For normal angle refinement
GLO [ang-steps] = '15,3.3, 3,2,2, 2,1.5,1.5,1.5,1.5, 1.5,1.5,1.5,1.5,1.5, 1.5,1.5,1.5,1.5,1.5' ; Angular degree steps
GLO [ang-limits] = '0,0, 15,15,8, 6,5,5,5,5, 5,5,5,5,5, 5,5,5,5,5' ; Angular limits
ELSE
; For SMALL angle refinement
GLO [ang-step-sm] = '(0.5)' ; Angular degree steps
GLO [theta-range] = '(2.0)' ; Theta range
ENDIF
; Following flag variables are used to activate OPTIONAL amplitude enhancement on each step
GLO [amp-enhance-flags] = '0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0' ; Amplitude enhancement selector
; ----------------- Input files --- May have to EDIT these names ------
GLO [params] = '../params' ; Parameter doc file (REQUIRED input file)
GLO [input_dir] = 'input/' ; Main dir. for input files (Used in prepare)
GLO [vol_orig] = '../Reconstruction/vol{**[iter]}' ; Initial reconstructed volume (reference volume)
GLO [sel_group_orig] = '../Reconstruction/sel_group_cclim' ; Group selection doc file
GLO [sel_particles_orig] = '../Reconstruction/sel_particles_{***[grp]}' ; Particle selection doc file
GLO [group_align_orig] = '../Alignment/align_{**[iter]}_{***[grp]}' ; Initial alignment parameter file (Used in prepare)
GLO [unaligned_images_orig] = '../Alignment/data{***[grp]}' ; Original unaligned images stack
; Following file is OPTIONAL - Only needed if using amplitude enhancement
GLO [scattering_doc] = 'input/scattering' ; OPTIONAL enhancement doc file
; -------------- Output files -- No need to edit for default refinement ----------
GLO [final_dir] = 'final/' ; Main dir. for output files
GLO [temp_work_dir] = 'work/' ; Temp work dir
GLO [temp_local_dir] = '/scratch/' ; OPTIONAL local disk scratch dir for PubSub use
GLO [start_vol] = 'input/vol01' ; Initial reconstructed volume copy
GLO [sel_group] = 'input/sel_group' ; Group selection doc file
GLO [sel_group_sorted] = 'input/sel_group_sort' ; Sorted group selection doc file
GLO [sel_particles] = 'input/sel_particles_{***[grp]}' ; Particle selection doc file
GLO [unaligned_images] = 'input/data{***[grp]}' ; Unaligned images stack (usually links)
GLO [current_vol] = 'final/vol{**[iter]}' ; Produced by 'AP SH' or previous iter.
GLO [next_vol] = 'final/vol{**[next-iter]}' ; Made for next iter.
GLO [next_val] = 'final/val{**[next-iter]}' ; Volumes
GLO [group_align] = 'final/align_{**[iter]}_{***[grp]}' ; Aignment parameter input file
GLO [next_group_align] = 'final/align_{**[next-iter]}_{***[grp]}' ; Alignment parameter output file
GLO [group_vol] = 'work/vol_{**[iter]}_{***[grp]}' ; Current group volumes
GLO [next_group_vol] = 'work/vol_{**[next-iter]}_{***[grp]}' ; Next group volumes
GLO [next_group_vol_template]= 'work/vol_{**[next-iter]}_***' ; Group volume template
IF ([small-ang] == 0) THEN
GLO [temp_ref_projs] = '[temp_local_dir]/refproj{**[iter]}_{***[grp]}' ; For temp. local scratch file (deleted)
ELSE
GLO [img_ang_vora] = 'final/angvora_{**[iter]}_{***[grp]}' ; For Small angles use only
GLO [temp_ref_projs] = '_5@' ; For Small angles temp. local scratch file (deleted)
ENDIF
GLO [temp_ctf_file] = 'input/ctf{***[grp]}' ; CTF correction files
GLO [temp_ctf_file_template] = 'input/ctf***' ; CTF correction file template
GLO [iter_vft] = 'final/vft{**[iter]}' ; Temp. vft file template
GLO [group_bpr] = 'final/bpr{**[iter]}_{***[grp]}' ; Group volume file
GLO [group_bpr_template] = 'final/bpr{**[next-iter]}_***' ; Group volume template
GLO [next_group_bpr] = 'final/bpr{**[next-iter]}_{***[grp]}' ; Group volume file
GLO [iter_refangs] = 'work/ang_refs_{**[iter]}' ; Iter. ref. angle file
GLO [iter_sel_refangs] = 'work/sel_ang_refs_{**[iter]}' ; Iter. ref. angle selection file
GLO [next_fsc] = 'final/fscdoc_{**[next-iter]}' ; FSC doc file
GLO [next_group_fsc] = 'final/fscdoc_{**[next-iter]}_{***[grp]}' ; Group FSC doc file
GLO [ofsc] = 'final/ofscdoc_{**[next-iter]}' ; Overall FSC doc file from 'BP R'
GLO [next_group_ofsc] = 'final/ofscdoc_{**[next-iter]}_{***[grp]}' ; Group FSC doc files from 'BP R'
GLO [grp_resol] = 'final/group_resolutions' ; Group resolution doc file
GLO [iter_resol] = 'final/resolutions' ; Overall resolution doc file
GLO [bpr] = 'final/bpr{**[next-iter]}' ; Refined output volume
GLO [enhance_doc] = 'work/enhance_doc_{**[next-iter]}' ; OPTIONAL Enhancement doc file output
GLO [ref_rings] = 'work/SCR_{**[iter]}_{***[grp]}' ; OPTIONAL Reference rings files output
; ------------ Should not need to alter following parameters retrieved from 'params' file ---------------
UD 5,[sp_pixsiz] ; Get pixelsize (A)
[params] ; Parameter doc file
UD 6,[sp_kev] ; Electron energy (kV)
[params] ; Parameter doc file
UD 17,[sp_winsiz] ; Get window size (pixels), used to find projection radius
[params] ; Parameter doc file
UD E ; End params doc file usage
; Calculate lambda (A) from electron voltage
[sp_lambda] = 12.398 / SQR([sp_kev] * (1022.0 + [sp_kev]))
[r2] = INT([diam]/(2.0*[sp_pixsiz])) ; Alignment radius (pixels) used in alignment search
; Ensure that sum of alignment radius + translation are within window dimensions
[ring-sh] = [r2] + [alignsh] ; Last ring + translation step
[maxrad] = INT([sp_winsiz]/2) - 1 ; Max. radius of object in window
IF ([ring-sh] .GE. [maxrad]) THEN
; Must reduce radius of outer ring, not translation step
[r2] = [maxrad] - [alignsh] - 2 ; Reduces rotational search radius
ENDIF
[prj-radius] = INT(([win-frac]*[sp_winsiz])/2.0 ) ; Convert fraction to radius in pixels
; ----------------- END BATCH HEADER ---------------------------------
RE
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