mrcImageMultiCTFCompensation

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mrcImageMultiCTFCompensation is Eos's Command that performs CTF Correction to multiple images.


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

/Eos/img/Input0.mrc 27000 2.1 200 0.1
/Eos/img/Input1.mrc 27000 2.1 200 0.1
/Eos/img/Input2.mrc 27000 2.1 200 0.1
/Eos/img/Input3.mrc 27000 2.1 200 0.1
Input0's image
Input0-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

255 (30, 25, 0)
21.8076
47.9133

0.748645
Input1's image
Input1-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

255 (30, 26, 0)
20.6895
47.2143

0.737723
Input2's image
Input2-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

255 (27, 32, 0)
19.0078
47.768

0.746374
Input3's image
Input3-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

255 (28, 33, 0)
18.3279
45.0774

0.704334


Example of options only essential

-o 's image
Outdata-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-950.729 (30, 33, 0)

91.5373 (61, 58, 0)
-199.582
202.06

3.15719
-f 's image
Outdata2-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.0117408 (32, 31, 0)

12773.2 (0, 0, 0)
30.7184
365.42

5.70969


Option -W

Case: W=0.5

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

Min

Max
Mean
SD

SE

-178.794 (29, 32, 0)

31.7025 (15, 31, 0)
-7.67623
35.9686

0.562009
-f 's image
Outdata2-W-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.000786083 (61, 50, 0)

656.031 (1, 0, 0)
5.93815
40.2896

0.629525


Option -WR

Case: WR=10.0, W=0.5

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

Min

Max
Mean
SD

SE

-153.883 (30, 32, 0)

23.7931 (15, 31, 0)
-7.67623
31.3292

0.489519
-f 's image
Outdata2-WR-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

9.05608e-06 (60, 32, 0)

587.065 (1, 0, 0)
4.29171
35.7021

0.557845


Option -SinWin

Case: SinWin=(0.05, 0.2)

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

Min

Max
Mean
SD

SE

-939.931 (30, 33, 0)

82.2886 (61, 59, 0)
-199.582
201.211

3.14392
-f 's image
Outdata2-SinWin-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (8, 0, 0)

12773.2 (0, 0, 0)
28.1205
365.158

5.70559


Option -ctfMode

Case: ctfMode=32

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

Min

Max
Mean
SD

SE

-1243.15 (30, 31, 0)

534.543 (1, 0, 0)
-7.92556e-07
404.255

6.31648
-f 's image
Outdata2-ctfMode32-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

12267.8 (1, 0, 0)
33.7224
477.688

7.46387


Case: ctfMode=256

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

Min

Max
Mean
SD

SE

-501.951 (1, 0, 0)

1288.01 (33, 32, 0)
-2.09152e-06
404.255

6.31648
-f 's image
Outdata2-ctfMode256-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

12267.8 (1, 0, 0)
33.7224
477.688

7.46387


Case: ctfMode=257

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

Min

Max
Mean
SD

SE

-50.4152 (5, 2, 0)

1009.22 (33, 32, 0)
199.582
202.06

3.15719
-f 's image
Outdata2-ctfMode257-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.0117408 (32, 31, 0)

12773.2 (0, 0, 0)
30.7184
365.42

5.70969


Option -m

Case: m=1, W=0.5

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

Min

Max
Mean
SD

SE

-175.249 (29, 32, 0)

49.852 (15, 31, 0)
-1.99391
37.3853

0.584145
-f 's image
Outdata2-m1-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00642588 (59, 34, 0)

681.324 (34, 0, 0)
6.41058
40.1134

0.626771
-log 's data
iter          0 : rms   -1.965984e+01 : min    1.000000e+06

Case: solventMode=1

-o 's image
Outdata-m1solventMode-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-220.728 (30, 32, 0)

42.9295 (15, 31, 0)
-9.08899
47.6864

0.7451
-f 's image
Outdata2-m1solventMode-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00745064 (63, 30, 0)

916.491 (1, 0, 0)
7.81324
53.2299

0.831717
-log 's data
iter          0 : rms   -3.997643e+00 : min    1.000000e+06


Case: solventSTD=2.0, solventMode=1

-o 's image
Outdata-m1solventSTD-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

342.42 (29, 32, 0)

552.916 (15, 31, 0)
513.538
35.9686

0.562009
-f 's image
Outdata2-m1solventSTD-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.000751982 (61, 50, 0)

32866.4 (0, 0, 0)
21.7463
726.986

11.3592
-log 's data
iter          0 : rms    7.485705e-01 : min    1.000000e+06
iter          1 : rms    3.354889e-01 : min    7.485705e-01
iter          2 : rms    2.279355e-01 : min    3.354889e-01
iter          3 : rms    1.763709e-01 : min    2.279355e-01
iter          4 : rms    1.463149e-01 : min    1.763709e-01
iter          5 : rms    1.267555e-01 : min    1.463149e-01
iter          6 : rms    1.130881e-01 : min    1.267555e-01
iter          7 : rms    1.030489e-01 : min    1.130881e-01
iter          8 : rms    9.539606e-02 : min    1.030489e-01
iter          9 : rms    8.939259e-02 : min    9.539606e-02


Case: MaxIter=5, solventSTD=2.0, solventMode=1

-o 's image
Outdata-m1MaxIter-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

107.285 (29, 32, 0)

317.781 (15, 31, 0)
278.402
35.9686

0.562009
-f 's image
Outdata2-m1MaxIter-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.000789315 (61, 50, 0)

17817.7 (0, 0, 0)
14.3983
395.41

6.17827
-log 's data
iter          0 : rms    7.485705e-01 : min    1.000000e+06
iter          1 : rms    3.354889e-01 : min    7.485705e-01
iter          2 : rms    2.279355e-01 : min    3.354889e-01
iter          3 : rms    1.763709e-01 : min    2.279355e-01
iter          4 : rms    1.463149e-01 : min    1.763709e-01


Case: m=16

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

Min

Max
Mean
SD

SE

-50.4152 (5, 2, 0)

1009.22 (33, 32, 0)
199.582
202.06

3.15719
-f 's image
Outdata2-m16-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.0117408 (32, 31, 0)

12773.2 (0, 0, 0)
30.7184
365.42

5.70969


Case: m=17

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

Min

Max
Mean
SD

SE

161250 (60, 60, 0)

1.85064e+06 (29, 32, 0)
432887
388639

6072.49
-f 's image
Outdata2-m17-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00899138 (31, 33, 0)

2.77048e+07 (0, 0, 0)
51930
757226

11831.7
-log 's data
iter          0 : rms    9.051428e-01 : min    1.000000e+06
iter          1 : rms    7.732108e-01 : min    9.051428e-01
iter          2 : rms    7.194946e-01 : min    7.732108e-01
iter          3 : rms    6.952064e-01 : min    7.194946e-01
iter          4 : rms    6.840820e-01 : min    6.952064e-01
iter          5 : rms    6.782160e-01 : min    6.840820e-01
iter          6 : rms    6.752780e-01 : min    6.782160e-01
iter          7 : rms    6.739355e-01 : min    6.752780e-01
iter          8 : rms    6.730211e-01 : min    6.739355e-01
iter          9 : rms    6.722654e-01 : min    6.730211e-01
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