([maxspfreq],[lambda],[iter1])
; Prepare for refinement run by initializing input
; and output directories
;
; SOURCE: prepare.pam
;
; PURPOSE: Prepare various initial files, CTF correction, etc.
;
; MASTER COPY: /net/bali/usr1/spider/docs/techs/recon/newprogs/
;
; CALLED FROM: refine & pub_refine refine.pam & pub_refine.pam
;
; INPUT REGISTERS (SET ABOVE):
; [maxspfreq] Maximum spatial frequency[a-1]
; [lambda] Lambda(angstroms)
; [iter] Initial iteration (usually 1)
;
; '***' denotes group
; INPUT FILES (SET IN refine_settings.pam):
; [start_vol] input/vol** Input volume file
; [order_select] input/order_select Group selection file
; [sel_particles] input/select_*** Particle selection files
; [start_group_align] input/align_01_*** Alignment parameter files
; [start_aligned_images] input/dala01_*** Aligned image stacks
;
; OUTPUT FILES (SET IN refine_settings.pam):
; [final_dir] final Directory
; [temp_work_dir] work Directory
; [temp[_local_dir] local Directory (Can be local on each node)
; [current_vol] final/vol01 Starting volume file (link)
; [sel_particles_odd] input/selectodd_*** Particle selection files
; [sel_particles_even] input/selecteven_*** Particle selection files
; [group_align] final/align_01_*** Group align input file
; [aligned_images_prefix] work/dala01_*** Aligned image stacks (link)
; [temp_ctf_file] input/ctf*** CTF correction files
;
; INLINE FILES USED: _1
[iter]=[iter1] ; Needed for naming initial files
VM ; Dir. for temporary files, local files and output files
mkdir -p [temp_work_dir] [temp_local_dir] [final_dir]
VM ; Put link to initial volume in final directory
ln -sf ../[start_vol].$DATEXT [current_vol].$DATEXT
FI [nsam] ; Query NSAM value (NROW must be = NSAM)
[current_vol] ; Initial reference volume (input)
12 ; NSAM location
UD N [num-grp] ; Get total number of defocus groups
[order_select]
[tot-part]=0
DO LB1 [i]=1,[num-grp] ; Loop over all groups
UD IC [i], [grp], [num-part] ; Get number of particles
[order_select] ; Doc file listing groups (input)
[tot-part]=[tot-part]+[num-part] ; Sum total number of particles in all groups
LB1
DO LB2 [i]=1,[num-grp] ; Loop over defocus groups ----------------------------------------
; GROUP, PART., DEFOCUS
UD IC [i], [grp], [num-part],[defocus] ; Get number of particles & defocus value=[defocus]
[order_select] ; Doc file listing groups (input)
VM ; Copy starting alignment parameter files to final dir.
cp [start_group_align].$DATEXT [group_align].$DATEXT
; Link the starting aligned images to work dir
VM ; Link from original dir. to work dir. (large files)
ln -sf ../[start_aligned_images].$DATEXT [aligned_images_prefix].$DATEXT
DOC SPLIT ; Split the particles into two sets of particle selection files
[sel_particles] ; Particle sel. doc file - input/select_***grp (input)
[sel_particles_odd] ; Particle sel. doc file - input/selectodd_***grp (output)
[sel_particles_even] ; Particle sel. doc file - input/selecteven_***grp (output)
; Create group CTFs
TF C3 ; Compute phase contrast transfer function
_1 ; Creates temp inline CTF file (output)
(2.0) ; CS
[defocus],[lambda] ; Defocus(Angstroems), lambda(Angstroems):
[nsam] ; Number of spatial freq. points
[maxspfreq] ; Maximum spatial frequency[a-1]
(0.005,0) ; Source size[a-1], defocus spread[a]
(0,0) ; Astigmatism[a], azimuth[deg]
(0.1,10000) ; Ampl contrast ratio [0-1], Gaussian env halfw [fou units]:
(-1) ; Sign
; Weight by avg. number of particles / group
[WT]=[num-grp]*[num-part]/[tot-part]
AR ; Weight CTF by number of particles
_1 ; Temp inline CTF file (input)
[temp_ctf_file] ; Weighted for CTF (output)
P1*[WT] ; Does the weighting
VM
echo ' 'Group: {***[grp]} CTF weighting: {%f8.2%[WT]}
LB2
UD ICE ; Finished with this doc file
[order_select]
DE ; Remove temp. inline file
_1
VM
echo ' Finished initial file preparation'
VM
echo ' '
RE
;