([radius],[maxspfreq],[iter])
;
; End of refinement
;
; SOURCE: spider/docs/techs/recon/newprogs/endrefine.pam
; New Nov 2000 ArDean Leith
; Filenames Dec 2009 ArDean Leith
; echo date Sep 2010 ArDean Leith
; softmask call Nov 2010 ArDean Leith
; softmask call active, nodala Jan 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):
; [radius] Radius of object
; [maxspfreq] Max. spatial frequency
; [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 volumes-overall
; [group_bpr_template]_sub1 final/bpr##+_***_sub1 Group volumes-sub1
; [group_bpr_template]_sub2 final/bpr##+_***_sub2 Group volumes-sub2
;
; OUTPUT FILES:
; [bpr] final/bpr##+ Final volume-overall
; [bpr]_sub1 final/bpr1##+_sub1 Final volumes-sub1
; [bpr]_sub2 final/bpr2##+_sub2 Final volumes-sub2
; [dbpr] final/dbpr##+ Final doc. file
;
;......................................................................
[softmask] = 1 ; Resolution volume masking
[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
[temp_ctf_file_template] ; Volume ctf files (input)
3.0 ; SNR
[bpr] ; Final volume-overall (output)
TF CTS ; CTF correction & vol. merge
[group_bpr_template]_sub1 ; Group volume-1 (input)
[sel_group] ; Group file numbers
[temp_ctf_file_template] ; Volume ctf files (input)
3.0 ; SNR
[bpr]_sub1 ; Final volume-1 (output)
TF CTS ; CTF correction & vol. merge
[group_bpr_template]_sub2 ; Group volume-2 (input)
[sel_group] ; Group file numbers
[temp_ctf_file_template] ; Volume ctf files (input)
3.0 ; SNR
[bpr]_sub2 ; Final volume-2 (output)
IF ([softmask].EQ.1) THEN ; Gaussian mask for resolution volumes
VM
echo " Using spherical softmask for resolution calculation"
@softmask([radius]) ; Pixel radius for masking
[bpr]_sub1 ; Final volume-1 (input)
[bpr]_sub2 ; Final volume-2 (input)
_13 ; Inline mask volume (output)
[bpr]_sub1 ; Masked volume-1 (output)
[bpr]_sub2 ; Masked volume-2 (output)
DE ; Delete incore mask volume
_13 ; Inline file (removed)
ENDIF
; Final volume resolution calculation
RF 3 [unused],[fsc] ; Phase Residual & FSC
[bpr]_sub1 ; Final volume-1 (input)
[bpr]_sub2 ; Final volume-2 (input)
0.5 ; Ring width
0.2, 2.0 ; Scale factor
C ; Missing cone
90.0 ; Max. tilt angle
3 ; Factor for noise comparision
[dbpr] ; Resolution doc. file (output)
; Record final volume resolution in doc. file
[val] = 0
@saveresp([maxspfreq],[iter],[val],[fsc])
[dbpr_resol] ; Resolution doc. file (output)
RE
;