mrcImageMultiCTFCompensation

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mrcImageMultiCTFCompensation is Eos's Command that performs CTF Correction to multiple images that have each other same field and different CTF. It outputs the average image of each image after CTF Correction.


List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: ASCII(File List) stdin
-info2 Optional Input: ASCII(File List) stdin
-o Essential Output(average): mrcImage stdout
-f Optional Output(average): mrcImage(FFT) stdout
-W Optional WhiteNoise(Noise/Signal) 1.0
-WR Optional WhiteNoiseRaising 1.0
-SinWin Optional sin Windowing (R[/A]): (SinWinRmin, SinWinRmax) (0.1, 1.0)
-MaxIter Optional Max Iteration 10
-ctfMode Optional CTFMode 1
-solventMode Optional If solvent flatterning is used, NEED 0
-solventSTD Optional If solvent flatterning is used as mode=1, NEED -1.0
-Log Optional Log File Name stderr
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　

-ctfMode details

Value Description
0 Phase Only
1 Phase and Amplitude
+32 With Illumination Angle
+256 As Absolute Value

-m details

Value Description
0 CTF-weighted compensation, CTF/(SQR(CTF) + (NS)^2)
+1 Adding solvent-flattening process
+16 Without phase flipping, in case of images after phase only correction.

-i format

filename0 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
filename1 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
     .                .            .           .                   .
     .                .            .           .                   .
     .                .            .           .                   .

-Info2 format

filename0.ctfinfo 
filename1.ctfinfo 
          .
          .
          .


Execution example

-i data

Original data's image
Input-B120.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

255 (49, 32, 0)
21.0538
47.6709

0.595886

Use simulation images that is multiplied each different CTF to above image, as input file. 

/Eos/img/Input-B120-CTF2.mrc 27000 2.1 200 0.1
/Eos/img/Input-B120-CTF3.mrc 9000 2.1 200 0.1
/Eos/img/Input-B120-CTF4.mrc 27000 2.1 400 0.1
/Eos/img/Input-B120-CTF5.mrc 27000 2.1 200 0.3
Input-B120-CTF2.mrc's image
Input-B120-CTF2.png

Min

Max
Mean
SD

SE

-67.2449 (35, 36, 0)

48.4524 (50, 51, 0)
-5.60279e-08
13.2796

0.165995

Input-B120-CTF2-Cnp.png
case: CTF Correction at single

Min

Max
Mean
SD

SE

-49.3218 (28, 26, 0)

133.566 (37, 38, 0)
8.98254e-07
26.7724

0.334655
Input-B120-CTF3.mrc's image
Input-B120-CTF3.png

Min

Max
Mean
SD

SE

-57.5666 (25, 38, 0)

53.971 (44, 29, 0)
-5.02996e-08
9.30611

0.116326

Input-B120-CTF3-Cnp.png
case: CTF Correction at single

Min

Max
Mean
SD

SE

-49.4192 (47, 51, 0)

137.108 (49, 32, 0)
5.49823e-07
19.7161

0.246452
Input-B120-CTF4.mrc's image
Input-B120-CTF4.png

Min

Max
Mean
SD

SE

-68.355 (24, 39, 0)

42.4746 (44, 26, 0)
-3.45941e-08
10.9018

0.136272

Input-B120-CTF4-Cnp.png
case: CTF Correction at single

Min

Max
Mean
SD

SE

-43.0975 (26, 31, 0)

117.683 (49, 32, 0)
4.44953e-07
22.9822

0.287278
Input-B120-CTF5.mrc's image
Input-B120-CTF5.png

Min

Max
Mean
SD

SE

-44.9091 (37, 36, 0)

26.5736 (28, 28, 0)
-2.71914e-08
8.97143

0.112143

Input-B120-CTF5-Cnp.png
case: CTF Correction at single

Min

Max
Mean
SD

SE

-33.0969 (49, 51, 0)

73.3827 (35, 37, 0)
-1.68364e-08
15.1195

0.188993


Case: Options only essential

-o 's image
Outdata-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-40.2801 (48, 52, 0)

104.151 (36, 38, 0)
1.24049e-07
18.8015

0.235019
-f 's image
Outdata2-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

7.30857e-06 (75, 37, 0)

378.143 (42, 0, 0)
4.45621
19.8824

0.24853

Option -W

Case: W=1

-o 's image
Outdata-W-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-17.0714 (27, 31, 0)

23.2441 (40, 52, 0)
5.81327e-09
4.65713

0.0582141
-f 's image
Outdata2-W-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

3.22907e-07 (0, 0, 0)

62.9461 (46, 78, 0)
1.28884
4.68843

0.0586053

Option -WR

Case: WR=10.0, W=0.5

-o 's image
Outdata-WR-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-11.5567 (27, 31, 0)

15.7516 (24, 39, 0)
1.23206e-08
3.24282

0.0405352
-f 's image
Outdata2-WR-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

2.72506e-08 (75, 37, 0)

45.7637 (46, 78, 0)
0.700623
3.33709

0.0417136

Option -SinWin

Case: SinWin=(0.05, 0.2)

-o 's image
Outdata-SinWin-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-39.9332 (48, 52, 0)

102.315 (36, 38, 0)
1.52273e-07
18.7407

0.234259
-f 's image
Outdata2-SinWin-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (40, 1, 0)

378.143 (42, 0, 0)
4.1815
19.8843

0.248553

Option -ctfMode

Case: ctfMode=32

-o 's image
Outdata-ctfMode32-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-24.2681 (68, 48, 0)

207.103 (36, 38, 0)
-1.0943e-09
45.5848

0.56981
-f 's image
Outdata2-ctfMode32-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1280.12 (41, 0, 0)
6.47008
51.7633

0.647041

Case: ctfMode=256

-o 's image
Outdata-ctfMode256-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-191.228 (36, 38, 0)

26.7763 (67, 30, 0)
-3.91243e-08
45.3127

0.566409
-f 's image
Outdata2-ctfMode256-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1280.12 (41, 0, 0)
5.38217
51.6411

0.645514

Case: ctfMode=257

-o 's image
Outdata-ctfMode257-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-90.5402 (36, 37, 0)

39.3153 (49, 51, 0)
-1.30477e-07
18.1267

0.226584
-f 's image
Outdata2-ctfMode257-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

1.17451e-06 (75, 37, 0)

378.143 (42, 0, 0)
3.33762
19.4523

0.243154

Option -m

Case: m=1, W=1

Case: No other settings
-o 's image
Outdata-m1-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-9.82557 (48, 51, 0)

92.1757 (49, 32, 0)
6.14297
14.8838

0.186048
-f 's image
Outdata2-m1-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00108315 (40, 41, 0)

491.438 (0, 0, 0)
4.1562
18.0735

0.225919
-log 's data
iter          0 : rms    1.013455e+01 : min    1.000000e+06
iter          1 : rms    1.355871e+00 : min    1.013455e+01
iter          2 : rms    8.647722e-01 : min    1.355871e+00
iter          3 : rms    6.229646e-01 : min    8.647722e-01
iter          4 : rms    4.844930e-01 : min    6.229646e-01
iter          5 : rms    3.971868e-01 : min    4.844930e-01
iter          6 : rms    3.377429e-01 : min    3.971868e-01
iter          7 : rms    2.951728e-01 : min    3.377429e-01
iter          8 : rms    2.629044e-01 : min    2.951728e-01
iter          9 : rms    2.370113e-01 : min    2.629044e-01
Case: solventMode=1
-o 's image
Outdata-m1solventMode-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-20.1029 (48, 51, 0)

87.1488 (49, 32, 0)
2.38926
14.7396

0.184245
-f 's image
Outdata2-m1solventMode-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00627302 (76, 14, 0

222.088 (42, 0, 0)
4.12707
15.7098

0.196372
-log 's data
iter          0 : rms    3.709238e+01 : min    1.000000e+06
iter          1 : rms    3.539059e+00 : min    3.709238e+01
iter          2 : rms    1.971014e+00 : min    3.539059e+00
iter          3 : rms    1.314187e+00 : min    1.971014e+00
iter          4 : rms    9.704149e-01 : min    1.314187e+00
iter          5 : rms    7.649823e-01 : min    9.704149e-01
iter          6 : rms    6.304888e-01 : min    7.649823e-01
iter          7 : rms    5.362647e-01 : min    6.304888e-01
iter          8 : rms    4.668152e-01 : min    5.362647e-01
iter          9 : rms    4.135905e-01 : min    4.668152e-01
Case: solventSTD=2.0, solventMode=1
-o 's image
Outdata-m1solventSTD-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

85.3666 (27, 31, 0)

146.065 (58, 33, 0)
101.654
5.9911

0.0748887
-f 's image
Outdata2-m1solventSTD-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00707058 (78, 44, 0)

8132.32 (0, 0, 0)
4.62714
143.824

1.7978
-log 's data
iter          0 : rms    1.424218e+00 : min    1.000000e+06
iter          1 : rms    2.156973e-01 : min    1.424218e+00
iter          2 : rms    1.394271e-01 : min    2.156973e-01
iter          3 : rms    1.043566e-01 : min    1.394271e-01
iter          4 : rms    8.473523e-02 : min    1.043566e-01
iter          5 : rms    7.243526e-02 : min    8.473523e-02
iter          6 : rms    6.412249e-02 : min    7.243526e-02
iter          7 : rms    5.819677e-02 : min    6.412249e-02
iter          8 : rms    5.380184e-02 : min    5.819677e-02
iter          9 : rms    5.044070e-02 : min    5.380184e-02
Case: MaxIter=5, solventSTD=2.0, solventMode=1
-o 's image
Outdata-m1MaxIter-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

35.7164 (27, 31, 0)

94.8793 (58, 33, 0)
52.0534
5.94982

0.0743728
-f 's image
Outdata2-m1MaxIter-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00307367 (71, 39, 0)

4164.28 (0, 0, 0)
3.33262
73.8045

0.922556
-log 's data
iter          0 : rms    1.424218e+00 : min    1.000000e+06
iter          1 : rms    2.156973e-01 : min    1.424218e+00
iter          2 : rms    1.394271e-01 : min    2.156973e-01
iter          3 : rms    1.043566e-01 : min    1.394271e-01
iter          4 : rms    8.473523e-02 : min    1.043566e-01

Case: m=16

-o 's image
Outdata-m16-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-90.5402 (36, 37, 0)

39.3153 (49, 51, 0)
-1.13944e-07
18.1267

0.226584
-f 's image
Outdata2-m16-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

1.17451e-06 (75, 37, 0)

378.143 (42, 0, 0)
3.33762
19.4523

0.243154

Case: m=17

-o 's image
Outdata-m17-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-363.432 (24, 39, 0)

64206.9 (50, 53, 0)
12232.5
12224.9

152.812
-f 's image
Outdata2-m17-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.000769818 (62, 30, 0)

978599 (0, 0, 0)
2152.97
21751

271.888
-log 's data
iter          0 : rms    2.228456e+00 : min    1.000000e+06
iter          1 : rms    1.072463e+00 : min    2.228456e+00
iter          2 : rms    8.595473e-01 : min    1.072463e+00
iter          3 : rms    7.822678e-01 : min    8.595473e-01
iter          4 : rms    7.485957e-01 : min    7.822678e-01
iter          5 : rms    7.339871e-01 : min    7.485957e-01
iter          6 : rms    7.188863e-01 : min    7.339871e-01
iter          7 : rms    7.127621e-01 : min    7.188863e-01
iter          8 : rms    7.096454e-01 : min    7.127621e-01
iter          9 : rms    7.069848e-01 : min    7.096454e-01
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