([r2],[pixsiz],[iter])
;
; End of refinement
;
; SOURCE: spider/docs/techs/recon/newprogs/endrefine.pam
; New Nov 2000 ArDean Leith
; Filenames Dec 2009 ArDean Leith
; softmask call Nov 2010 ArDean Leith
; softmask active, nodala Jan 2012 ArDean Leith
; FSC Aug 2012 ArDean Leith
; FSC mask Sep 2012 ArDean Leith
;
; PURPOSE: Corrects group volumes for CTF and merges them into a
; final output volume. Computes final reconstruction resolution.
;
; CALLED FROM: refine.pam
;
; INPUT REGISTERS (SENT FROM CALLER):
; [r2] Radius of object
; [pixsiz] Pixel size
; [iter] Current iteration
;
; '##' denotes iteration, '##+' denotes next iteration, '***' denotes group
; INPUT FILES
; [sel_group] input/sel_group Group selection file
; [temp_ctf_file_template] work/ctf*** Group CTF correction files
; [group_bpr_template] final/bpr##+_*** Group overall volumes
; [group_bpr_template]_sub1 final/bpr##+_***_sub1 Group subset volumes-1
; [group_bpr_template]_sub2 final/bpr##+_***_sub2 Group subset volumes-2
;
; OUTPUT FILES:
; [bpr] final/bpr##+ Final overall volume
; [bpr]_sub1 final/bpr1##+_sub1 Final subset volume-1
; [bpr]_sub2 final/bpr2##+_sub2 Final subset volume-2
; [ofsc] final/ofscdoc_##+ Overall FSC doc file
; [iter_resol] final/resolutions Resolution doc file
;
;......................................................................
[next-iter] = [iter] + 1
VM
echo ' '; echo -n " Starting endrefine, Iteration: {**[iter]} --- "; date '+ %x %X'
TF CTS ; CTF correction & vol. merge
[group_bpr_template] ; Group volumes (input)
[sel_group] ; Group file numbers (input)
[temp_ctf_file_template] ; Volume ctf files (input)
3.0 ; SNR
[bpr] ; Final overall volume (output)
TF CTS ; CTF correction & vol. merge
[group_bpr_template]_sub1 ; Group volume-1 (input)
[sel_group] ; Group file numbers (input)
[temp_ctf_file_template] ; Volume ctf files (input)
3.0 ; SNR
[bpr]_sub1 ; Final subset volume-1 (output)
TF CTS ; CTF correction & vol. merge
[group_bpr_template]_sub2 ; Group volume-2 (input)
[sel_group] ; Group file numbers (input)
[temp_ctf_file_template] ; Volume ctf files (input)
3.0 ; SNR
[bpr]_sub2 ; Final subset volume-2 (output)
; Resolution calculation
FSC [half],[spfreq],[res] ; Find phase residual & shell correl.
[bpr]_sub1 ; Final subset volume-1 (input)
[bpr]_sub2 ; Final subset volume-2 (input)
0.5,[r2] ; Shell width, mask radius
[pixsiz] ; Pixel size
[ofsc] ; Overall FSC doc file (output)
* ; No Gnuplot file
; Record final volume resolution in doc. file
[gr] = 0 ; Not for a defocus group
SD [iter],[iter],[gr],[res] ; Save resolution
[iter_resol] ; Resolution doc file (output)
RE
;