forked from nogaleslab/Microtubule
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathmult_hreconstruct_n_C1.com
99 lines (95 loc) · 4.35 KB
/
mult_hreconstruct_n_C1.com
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
#!/bin/csh -f
#unlimit
limit coredumpsize 0
set working_directory = `pwd`
set SCRATCH = `pwd`
cd $SCRATCH
set bin_dir = /home/zhangrui/bin/frealign_v9.09/bin
set start = $3
cp mparameters_run mparameters_run_${start}
@ prev = $start - 1
set data_input = `grep data_input mparameters_run | awk '{print $2}'`
set raw_images = `grep raw_images_low mparameters_run | awk '{print $2}'`
if ( $raw_images == "" ) set raw_images = `grep raw_images mparameters_run | awk '{print $2}'`
set raw_images = `echo ${raw_images:r}`
set extension = `ls $raw_images.* | head -1`
if ( $extension == "" ) then
set raw_images = ${working_directory}/${raw_images}
set extension = `ls $raw_images.* | head -1`
endif
set extension = `echo ${extension:e}`
set thresh = `grep thresh_reconst mparameters_run | awk '{print $2}'`
set pbc = `grep PBC mparameters_run | awk '{print $2}'`
# set boff = `grep BOFF mparameters_run | awk '{print $2}'`
set dang = `grep DANG mparameters_run | awk '{print $2}'`
set itmax = `grep ITMAX mparameters_run | awk '{print $2}'`
set mode = `grep MODE mparameters_run | awk '{print $2}'`
set FFILT = `grep FFILT mparameters_run | awk '{print $2}'`
set FBEAUT = `grep FBEAUT mparameters_run | awk '{print $2}'`
set rrec = `grep res_reconstruction mparameters_run | awk '{print $2}'`
set rref = `grep res_high_refinement mparameters_run | awk '{print $2}'`
set rclas = `grep res_high_class mparameters_run | awk '{print $2}'`
set rbf = `grep RBfactor mparameters_run | awk '{print $2}'`
set sym = `grep Symmetry mparameters_run | awk '{print $2}'`
set alpha = `grep ALPHA mparameters_run | awk '{print $2}'`
set rise = `grep RISE mparameters_run | awk '{print $2}'`
set nsub = `grep NSUBUNITS mparameters_run | awk '{print $2}'`
set nstart = `grep NSTARTS mparameters_run | awk '{print $2}'`
set stiff = `grep STIFFNESS mparameters_run | awk '{print $2}'`
set pix = `grep pix_size mparameters_run | awk '{print $2}'`
set rrec = `echo $rrec $pix | awk '{if ($1+0.0 == 0.0) {print 2.1*$2} else {print $1} }'`
set kV = `grep Voltage mparameters_run | awk '{print $2}'`
set AmpC = `grep Amp_contrast mparameters_run | awk '{print $2}'`
set ImC = `grep image_contrast mparameters_run | awk '{print $2}'`
if ( ! $status ) then
if ( $ImC == "P" ) set AmpC = `echo -$AmpC`
endif
set dstep = `grep dstep mparameters_run | awk '{print $2}'`
set ro = `grep outer_radius mparameters_run | awk '{print $2}'`
set ri = `grep inner_radius mparameters_run | awk '{print $2}'`
set MW = `grep mol_mass mparameters_run | awk '{print $2}'`
set cs = `grep Aberration mparameters_run | awk '{print $2}'`
set mp_cpus = `grep mp_cpus mparameters_run | awk '{print $2}'`
#
set m = ""
if ( ${mp_cpus} > 1 ) then
set m = "_mp"
setenv NCPUS ${mp_cpus}
setenv OMP_NUM_THREADS ${mp_cpus}
endif
set form = `${bin_dir}/fheader.exe ${raw_images}.${extension} | grep --binary-files=text Opening | awk '{print $2}'`
set fm = "M"
if ( $form == "SPIDER" ) set fm = "S"
if ( $form == "IMAGIC" ) set fm = "I"
#
\rm ${data_input}_${start}_r${4}_n${1}.${extension}
\rm ${data_input}_${start}_r${4}_n${1}.res
time ${bin_dir}/frealign_v9_mp.exe << eot >& ${data_input}_mult_reconstruct_r${4}_n${1}.log
M,0,F,F,F,F,0,${FBEAUT},${FFILT},F,F,0,F,2,1 !CFORM,IFLAG,FMAG,FDEF,FASTIG,FPART,IEWALD,FBEAUT,FFILT,FBFACT,FMATCH,IFSC,FDUMP,IMEM,INTERP
${ro},${ri},${pix},${MW},${AmpC},0.0,${pbc},0.0,10.,1,10 !RO,RI,PSIZE,WGH,XSTD,PBC,BOFF,DANG,ITMAX,IPMAX
1 1 1 1 1 !MASK
${1},${2} !IFIRST,ILAST
0 !ASYM symmetry card (I=icosahedral)
1.,${dstep},60.0,${thresh},${cs},${kV},0.0,0.0 !RELMAG,DSTEP,TARGET,THRESH,CS,AKV,TX,TY
${rrec}, 200.0, ${rref}, ${rclas}, 100.0, ${rbf} !RREC,RMIN,RMAX,RCLAS,DFSTD,RBFACT
${raw_images}.${extension}
/dev/null
${working_directory}/${data_input}_${start}_r${4}.par
${data_input}_${start}_r${4}.res
${data_input}_${start}_r${4}_n${1}.shft
0., 0., 0., 0., 0., 0., 0., 0. ! terminator with RELMAG=0.0
${data_input}_${start}_r${4}_n${1}.${extension}
${data_input}_${start}_r${4}_weights
${data_input}_${start}_r${4}_map1.${extension}
${data_input}_${start}_r${4}_map2.${extension}
${data_input}_${start}_r${4}_phasediffs
${data_input}_${start}_r${4}_pointspread
eot
#
\rm ${data_input}_${start}_r${4}_weights
\rm ${data_input}_${start}_r${4}_n${1}.shft
\rm ${data_input}_${start}_r${4}_phasediffs
\rm ${data_input}_${start}_r${4}_pointspread
#
echo 'mreconstruct.com finished' >> ${data_input}_mult_reconstruct_r${4}_n${1}.log
date