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tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revision939d0a0c813cbd33fb07633aabbafa70af7d0537 (tree)
Time2014-09-01 16:43:53
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

Add tutorial data of CTF Correction
new file: CTFCorrection/CTFCorrection1/Makefile
new file: CTFCorrection/CTFCorrection1/example.tif

Change Summary

Incremental Difference

--- /dev/null
+++ b/CTFCorrection/CTFCorrection1/Makefile
@@ -0,0 +1,153 @@
1+.SUFFIXES: .tif .mrc .cen .nor .fft .ctfinfoauto \
2+ .ctfinfo .ctf .ctfps
3+
4+-include TIFS
5+-include MRCS
6+-include CENS
7+-include NORS
8+-include FFTS
9+-include CTFAutoList
10+-include CTFInfoList
11+-include CTFS
12+
13+#
14+# Setting Parameter
15+# [A/pixel]
16+RESOLUTION=3.80
17+
18+# JOB Number
19+JN=-j 4
20+
21+#####################
22+Help::
23+ @echo "----- How To Use -----"
24+ @echo "1. Prepare files(xxxx.tif) to be analyzed."
25+ @echo "2. make TIF2CTF"
26+ @echo ""
27+ @echo "--- Special Target ---"
28+ @echo "make DispCEN"
29+ @echo "make DispCTF"
30+ @echo "make PrintCTF"
31+ @echo ""
32+ @echo "--- Current Parameter ---"
33+ @echo "RESOLUTION: $(RESOLUTION) [A/pixel]"
34+ @echo "Job number for make: $(JN)"
35+
36+mrc: $(TIFS:.tif=.mrc)
37+cen: $(MRCS:.mrc=.cen)
38+nor: $(CENS:.cen=.nor)
39+fft: $(NORS:.nor=.fft)
40+ctfinfoauto: $(FFTS:.fft=.ctfinfoauto)
41+ctfinfo: $(CTFAutoList:.ctfinfoauto=.ctfinfo)
42+ctf: $(CTFInfoList:.ctfinfo=.ctf)
43+ctfps: $(CTFInfoList:.ctfinfo=.ctfps)
44+
45+TIF2CTF::
46+ make TIFS; make $(JN) mrc;
47+ make MRCS; make $(JN) cen;
48+ make CENS; make $(JN) nor;
49+ make NORS; make $(JN) fft;
50+ make FFTS; make $(JN) ctfinfoauto;
51+ make CTFAutoList; make ctfinfo;
52+ make CTFInfoList; make $(JN) ctf;
53+ make CTFS
54+
55+TIFS::
56+ echo "TIFS=\\" > TIFS
57+ ls -1 *.tif | sed s/tif/tif\\\\/ >> TIFS
58+ echo "" >> TIFS
59+
60+MRCS::
61+ echo "MRCS=\\" > MRCS
62+ ls -1 *.mrc | sed s/mrc/mrc\\\\/ >> MRCS
63+ echo "" >> MRCS
64+
65+CENS::
66+ echo "CENS=\\" > CENS
67+ ls -1 *.cen | sed s/cen/cen\\\\/ >> CENS
68+ echo "" >> CENS
69+
70+NORS::
71+ echo "NORS=\\" > NORS
72+ ls -1 *.nor | sed s/nor/nor\\\\/ >> NORS
73+ echo "" >> NORS
74+
75+FFTS::
76+ echo "FFTS=\\" > FFTS
77+ ls -1 *.fft | sed s/fft/fft\\\\/ >> FFTS
78+ echo "" >> FFTS
79+
80+CTFAutoList::
81+ echo "CTFAutoList=\\" > CTFAutoList
82+ ls -1 *.ctfinfoauto | sed s/ctfinfoauto/ctfinfoauto\\\\/ >> CTFAutoList
83+ echo "" >> CTFAutoList
84+
85+CTFInfoList::
86+ echo "CTFInfoList=\\" > CTFInfoList
87+ ls -1 *.ctfinfo | sed s/ctfinfo/ctfinfo\\\\/ >> CTFInfoList
88+ echo "" >> CTFInfoList
89+
90+CTFS::
91+ echo "CTFS=\\" > CTFS
92+ ls -1 *.ctf | sed s/ctf/ctf\\\\/ >> CTFS
93+ echo "" >> CTFS
94+
95+.tif.mrc:
96+ tiff2mrc -i $*.tif -o $*.mrc -r $(RESOLUTION) -m 0
97+
98+.mrc.cen:
99+ mrcImageCenterGet -i $*.mrc -o $*.cen -Nx 1000 -Ny 1000
100+
101+DispCEN:
102+ for i in $(CENS) ;\
103+ do \
104+ echo $$i;\
105+ Display2 -i $$i;\
106+ done
107+
108+.cen.nor:
109+ mrcImageAbnormalValueRemove -i $*.cen -o $*.nor -u 65535 16384 -m 1
110+
111+.nor.fft:
112+ mrcImageFFT -i $*.nor -o $*.fft
113+
114+.fft.ctfinfoauto:
115+ ctfDetermine -i $*.fft -o $*.ctfinfoauto -D 50000 -m 128 \
116+ -CutLow 0.025 -CutHigh 0.15 -d 3 -Cc 0.7 -Cs 2.1
117+
118+.ctfinfoauto.ctfinfo:
119+ if [ ! -f $*.ctfinfo ] ; then \
120+ if [ -f default.ctfinfo ] ; then \
121+ cat default.ctfinfo >> $*.ctfinfo ; \
122+ else \
123+ cat $*.ctfinfoauto >> $*.ctfinfo ; \
124+ fi \
125+ fi
126+ ctfDisplay -i $*.fft
127+ mv $@ $@.tmp
128+ grep .: $@.tmp > $@
129+ awk '!/.ctfinfo/ {print $$0}' $@ > default.ctfinfo
130+
131+.ctfinfo.ctf:
132+ mv $*.ctfinfo $*.ctfinfo.tmp2
133+ grep .: $*.ctfinfo.tmp2 > $*.ctfinfo
134+ mrcImageCTFCompensation -i $*.fft -info2 $*.ctfinfo -o $*.ctf -m 1
135+
136+.ctf.ctfps:
137+ mrcImagePrint -i $*.ctf -o $*.ctfps -I -A -m 17 -S 0.08
138+
139+DispCTF:
140+ for i in $(CTFS) ;\
141+ do \
142+ echo $$i;\
143+ Display2 -i $$i -Inverse;\
144+ done
145+
146+PrintCTF:
147+ for i in $(CTFS) ;\
148+ do \
149+ echo $$i;\
150+ if [ -f $$i ] ; then \
151+ make `basename $$i .ctf`.ctfps; \
152+ fi \
153+ done
\ No newline at end of file
Binary files /dev/null and b/CTFCorrection/CTFCorrection1/example.tif differ
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