([maxspfreq],[radius],[alignsh],[prj-radius],[iter1],[iter-end],[lambda],[small-ang],[winsize],[converg])
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; Sets refinement parameters and files
;
; SOURCE: refine_settings.pam ArDean Leith Jul 2002
; [] ArDean Leith Dec 2005
; Rewritten More stacks ArDean Leith Dec 2006
;
; MASTER COPY: /net/bali/usr1/spider/dev/refine/
;
; INPUT REGISTERS:
;
; OUTPUT REGISTERS (SET BELOW):
; [maxspfreq] Maximum spatial freq (1/A)
; [radius] Radius of structure (pixels)
; [alignsh] Alignment shift +- allowed (pixels)
; [prj-radius] Projection radius (pixels)
; [iter1] Starting iteration
; [iter-end] Ending iteration
; [lambda] Lambda (Angstroms)
; [small-ang] Small angle refinement flag (1 is true)
; [winsize] Image or window size = volume size
; [converg] Convergence criterion fraction
;
; ============== DO NOT COPY FROM WEB BROWSER ==============
; ---------Try to set Refinement parameters from parameter file ----------
;
FR G
[params]input/params ; Parameter doc file
UD 5,[pixsize] ; Get pixelsize (Angstroms/pixel) (.17730)
[params] ; Parameter doc. file
UD 6,[kev] ; Electron energy (kV)
[params] ; Parameter doc. file
UD 14,[lambda] ; Get Lambda (Angstroms)
[params] ; Parameter doc. file
UD 15,[maxspfreq] ; Get maximum spatial frequency (1/Angstroms)
[params] ; Parameter doc. file
UD 17,[winsize] ; Get windowsize (Pixels), used to find projection radius
[params] ; Parameter doc. file
UD E ; End params doc. file usage
; ---- Adjust these parameters for your project --------------------- EDIT -----
[alignsh] = 6 ; Alignment shift (pixels) searched is +- this value
[iter1] = 1 ; Starting alignment step (iteration)
[iter-end] = 3 ; Ending alignment step (iteration)
[diam] = 349 ; Diameter of the structure (Angstroms) used in alignment search.
; (Default 276A is for ribosome. EDIT as needed.)
; This diameter is used to find radius for last alignment ring.
[win-frac] = 0.95 ; Fraction of window diameter used in projection (.95= use 95% window size)
[converg] = 0.05 ; Convergence criterion fraction
; Converges when [converg] % of all images move < 1.5 * stepsize.
[small-ang] = 0 ; For SMALL angle refinement set this to 1
IF ([small-ang].EQ.1) THEN
; For SMALL angle refinement
FR G ; Angular degree step (CAN EDIT THIS)
[ang-steps](0.5)
FR G ; Restriction on ang. search degrees (CAN EDIT THIS)
[ang-limits](2.0)
ELSE
FR G ; Angular degree steps (CAN EDIT THIS)
[ang-steps]2.0,2.0,2.0,2.0,2.0,1.5,1.5,1.5,1.5,1.5,1.5
FR G ; Restriction on ang. search degrees (CAN EDIT THIS)
[ang-limits]0.0,15.0,8.0,6.0,5.0,5.0,5.0,5.0,5.0,5.0,5.0
ENDIF
FR G ; Amplitude enhancement selector (CAN EDIT THIS)
[amp-enhance-flags]0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
; ---- Should not need to adjust following parameters --------------------------
[radius] = INT([diam]/(2.0*[pixsize])) ; Alignment radius (pixels) used in alignment search
; Ensure that sum of alignment radius + translation are within window dimensions
[ring-sh] = [radius] + [alignsh] ; Last ring + translation step
[maxrad] = INT([winsize]/2) - 1 ; Max. radius of object within window
IF ([ring-sh].GE.[maxrad]) THEN
; Must reduce alignment radius (last ring), not translation step
[radius] = [maxrad] - [alignsh] - 1 ; Reduces alignment radius
ENDIF
[prj-radius] = INT(([win-frac]*[winsize])/2.0 ) ; Convert fraction to radius in pixels
; If maximum spatial frequency is not given, compute it from pixel size in params file
IF ([maxspfreq].LE.0) [maxspfreq] = 1.0 / (2.0 * [pixsize])
; If Lambda is not given, compute it from electron energy in params file
IF ([lambda].LE.0) [lambda] = 12.398 / SQR([kev] * (1022.0 + [kev]))
; ============== DO NOT COPY FROM WEB BROWSER ==============
; ----------------- Input files --- May have to EDIT these names ------
FR G
[input_dir]input/ ; Main dir. for input files
FR G
[params]input/params ; Parameter doc file
FR G
[order_select]input/order_select ; Group selection doc file
FR G
[sorted_order_select]input/order_select_sort ; Sorted group selection doc file
FR G
[start_vol]input/vol{**[iter]} ; Initial reconstructed volume
FR G
[sel_particles]input/select_{***[grp]} ; Particle selection doc file
FR G
[start_group_align]input/align_{**[iter]}_{***[grp]} ; Alignment parameter file
FR G
[unaligned_images]input/data{***[grp]} ; Original unaligned images stack
FR G
[start_aligned_images]input/dala{**[iter]}_{***[grp]} ; Initial aligned images prefix
; Following two files OPTIONAL (only needed if using amplitude enhancement)
FR G
[scattering_doc]input/scattering ; OPTIONAL enhancement document input
FR G
[mask]input/mask ; OPTIONAL Mask for amplitude enhancement
; -------------- Output files -- No need to edit for default refinement ----------
FR G
[final_dir]final/ ; Main dir. for output files
FR G
[temp_local_dir]/tmp/ ; A local disk scratch dir
FR G
[temp_work_dir]work/ ; Temp work dir
FR G
[sel_particles_odd]input/selectodd_{***[grp]} ; Particle selection doc file
FR G
[sel_particles_even]input/selecteven_{***[grp]} ; Particle selection doc file
FR G
[current_vol]final/vol{**[iter]} ; Produced by 'AP SH' or previous iter.
FR G
[next_vol]final/vol{**[next-iter]} ; Made for next iter.
FR G
[next_val]final/val{**[next-iter]} ; Volumes
FR G
[group_align]final/align_{**[iter]}_{***[grp]} ; Aignment parameter input file
FR G
[next_group_align]final/align_{**[next-iter]}_{***[grp]} ; Alignment parameter output file
FR G
[aligned_images_prefix]work/dala{**[iter]}_{***[grp]} ; Current aligned images prefix
FR G
[aligned_images][aligned_images_prefix]@ ; Current aligned images in stack
FR G
[next_aligned_images]work/dala{**[next-iter]}_{***[grp]}@ ; Next aligned images stack
; -------------------------
FR G
[group_vol]work/vol_{**[iter]}_{***[grp]} ; Current group volume.
FR G
[next_group_vol]work/vol_{**[next-iter]}_{***[grp]} ; Next group volume.
FR G
[next_group_vol_template]work/vol_{**[next-iter]}_*** ; Group volume template
IF ([small-ang].EQ.0) THEN
FR G
[temp_ref_projs][temp_local_dir]/refproj{**[iter]}_{***[grp]} ; For Temporary local output file (deleted)
ELSE
FR G
[img_ang_vora]final/angvora_{**[iter]}_{***[grp]} ; For SMALL angles use only
FR G
[temp_ref_projs]_5@ ; For SMALL angles Temporary local output file (deleted)
ENDIF
FR G
[next_dres]final/dres{**[next-iter]} ; Next dres output doc. file
FR G
[temp_ctf_file]input/ctf{***[grp]} ; CTF correction files
FR G
[temp_ctf_file_template]input/ctf*** ; CTF correction file template
FR G
[iter_vft]final/vft{**[iter]} ; Temp. vft file template
FR G
[group_bpr]final/bpr{**[iter]}_{***[grp]} ; Group volume file
FR G
[group_bpr_template]final/bpr{**[next-iter]}_*** ; Group volume template
FR G
[next_group_bpr]final/bpr{**[next-iter]}_{***[grp]} ; Group volume file
FR G
[iter_ang_voea]work/angvoea_{**[iter]} ; Iter. angle voea file
FR G
[iter_select_voea]work/selvoea_{**[iter]} ; Iter. angle voea selection file
FR G
[next_group_dres]final/dres{**[next-iter]}_{***[grp]} ; Group dres output doc. file
FR G
[dbpr]final/dbpr{**[next-iter]} ; Output resolution doc files
FR G
[next_group_dbpr]final/dbpr{**[next-iter]}_{***[grp]} ; Output group resolution doc files
FR G
[dbpr_resol]final/resolutions ; Output resolution doc file
FR G
[grp_resol]final/group_resolutions ; Output resolution doc file
FR G
[bpr]final/bpr{**[next-iter]} ; Refined output volume
FR G
[enhance_doc]work/enhance_doc_{**[next-iter]} ; Enhancement document output
; ----------------- END BATCH HEADER ---------------------------------
RE
;