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tutorial: Commit

This repository is for tutorials of Eos.


Commit MetaInfo

Revision56a4d4d4ca99fbc1ffefc53bef5a860a4f026daf (tree)
Time2014-09-10 16:07:51
Authorkinoshita-eos <kinoshita@yasu...>
Commiterkinoshita-eos

Log Message

Modify: Change inverse before CTF file name
modified: CTFCorrection/CTFCorrection2/Makefile
Add: one tutorial data of CTF Correction.
new file: CTFCorrection/CTFCorrection3/Makefile

Change Summary

Incremental Difference

--- a/CTFCorrection/CTFCorrection2/Makefile
+++ b/CTFCorrection/CTFCorrection2/Makefile
@@ -95,7 +95,7 @@ ProcessForInput::
9595 make $(INPUT).$(CTF_2D_EXT);
9696 ln -s $(INPUT).$(CTF_2D_EXT) $(INPUT).mrc;
9797 mrc2tiff -i $(INPUT).$(INPUT_2D_EXT) -o $(INPUT)_org.tiff;
98- mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT).tiff -I;
98+ mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT)_i.tiff -I;
9999 mrc2tiff -i $(INPUT).$(CTF_2D_EXT) -o $(INPUT).tif;
100100
101101
--- /dev/null
+++ b/CTFCorrection/CTFCorrection3/Makefile
@@ -0,0 +1,84 @@
1+#
2+# This is Maikefile for CTF Correction Demo.
3+#
4+
5+#### Input extention ####
6+
7+#### Suffixes rule ####
8+.SUFFIXES: .ctfinfoauto2 .ctfinfo1
9+
10+#### INCLUDE ####
11+#-include ../CTFCorrection1/Makefile
12+-include ../CTFCorrection2/Makefile
13+#-include Makefile.common
14+#-include Makefile.common2
15+-include CTFAuto2List
16+-include CTFInfo1List
17+
18+#### Definition ####
19+
20+
21+#### Rules of the list created ####
22+ctfinfoauto2: $(FFTS:.fft=.ctfinfoauto2)
23+ctfinfo1: $(CTFAuto2List:.ctfinfoauto2=.ctfinfo1)
24+
25+CTFAuto2List::
26+ echo "CTFAuto2List=\\" > CTFAuto2List
27+ ls -1 *.ctfinfoauto2 | sed s/ctfinfoauto2/ctfinfoauto2\\\\/ >> CTFAuto2List
28+ echo "" >> CTFAuto2List
29+
30+CTFInfo1List::
31+ echo "CTFInfo1List=\\" > CTFInfo1List
32+ ls -1 *.ctfinfo1 | sed s/ctfinfo1/ctfinfo1\\\\/ >> CTFInfo1List
33+ echo "" >> CTFInfo1List
34+
35+##### Commands #####
36+all1::
37+# make InitialCTFDataFromPDB;
38+ make InitialSiemensStar;
39+# make InitialCTFDataFromMRC;
40+ make ProcessForInput;
41+ make ProcessForInput2;
42+ make TIF2CTF2;
43+ make $(INPUT).tiff
44+ make $(INPUT)-2.tiff
45+ make ImageAverage;
46+
47+ProcessForInput2::
48+ mrcImageCTFObservation -i $(INPUT).$(INPUT_2D_EXT) -o $(INPUT)-2.$(CTF_2D_EXT) -df 9000;
49+ ln -s $(INPUT)-2.$(CTF_2D_EXT) $(INPUT)-2.mrc;
50+ mrc2tiff -i $(INPUT)-2.$(INPUT_2D_EXT) -o $(INPUT)-2_org.tiff;
51+ mrc2tiff -i $(INPUT)-2.$(CTF_2D_EXT) -o $(INPUT)-2_i.tiff -I;
52+ mrc2tiff -i $(INPUT)-2.$(CTF_2D_EXT) -o $(INPUT)-2.tif;
53+
54+TIF2CTF2::
55+ make TIFS; make $(JN) mrc;
56+ make MRCS; make $(JN) cen;
57+ make CENS; make $(JN) nor;
58+ make NORS; make $(JN) fft;
59+ make FFTS;
60+ make $(JN) ctfinfoauto2;
61+ make CTFAutoList; make ctfinfo;
62+# touch $(INPUT).ctfinfo
63+# touch $(INPUT)-2.ctfinfo
64+ make CTFInfoList; make $(JN) ctf;
65+# make CTFS;
66+
67+ImageAverage::
68+ touch CTF_LIST;
69+ rm CTF_LIST;
70+ ls -1 *.ctf >> CTF_LIST;
71+ mrcImageAverage -i CTF_LIST -o $(INPUT).avg;
72+ mrc2tiff -i $(INPUT).avg -o $(INPUT)_avg.tiff;
73+
74+##### Commands(Input to Output) #####
75+.fft.ctfinfoauto2:
76+ ctfDetermine -i $*.fft -o $*.ctfinfoauto2 -D 27000 \
77+ -CutLow 0.025 -CutHigh 0.15 -d 3 -Cc 0.7 -Cs 2.1 \
78+ -BofMTF 1 -Ai 0.14 -Noise 0.2 -I0 1.3;
79+ mv $*.ctfinfoauto2 $*.ctfinfoauto;
80+
81+.ctfinfoauto2.ctfinfo1:
82+ cat $*.ctfinfoauto2 >> $*.ctfinfo1 ;
83+ mv $*.ctfinfo1 $*.ctfinfo;
84+
\ No newline at end of file
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