mrcImageCTFDetermination

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mrcImageCTFDetermination is Eos's Command for the estimation of the CTF. It outputs average phase difference with reference image or determined CTF Information. These data can be used as set data(-o) of ctfDisplay.


List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: mrcImage(M=0, 1: FFT, M=2: 2D) NULL
-r Essential Reference: mrcImage(M=0: FFT, M=1: llData, M=2: 2D) NULL
-o Optional Output: Optimum: ASCII(For M=0)
(defocus amplitude-contrast): minimum point		 stdout
-oP Optional Output: Distribution((-df) x (-AoverP)): mrcImage(For M=0) NULL
-oC Optional Output: CTF information: ASCII(using -mC) NULL
-oF Optional Output: Result FFT: mrcImage(For M=2) NULL
-kV Optional Acceleration voltage: [kV] 200
-Cs Optional Spherical aberration coefficient: [mm] 2.1
-Ain Optional IlluminationAperture[mrad] 0.02
-W Optional WhiteNoise(Noise/Signal) 1.0
-df Optional Defocus: [A]: (mindf, maxdf, deldf) (0.0, 200000, 1000)
-AoverP Optional AoverP[A] for in(minAoverP, maxAoverP, delAoverP) (0.0, 1.0, 0.01)
-Rmin Optional Min spatial frequency[/A] 0.0
-Rmax Optional Max spatial frequency[/A] 0.1
-mF Optional :Filter Type 1
-mW Optional Wight Type 0
-mS Optional Sum Type 0
-mC Optional CTF Information Type 0
-M Optional ref Type 0
-PixelSize Optional Pixel size [A] (For M=1) 5
-Width Optional Pad Width [pixel] (For M=1) 120
-truePitch Optional True Pitch [A] (For M=1) 700
-dfRef Optional dfRef for ref(firstDf, withinDf) (For M=2) (70000, 1000)
-AoverPRef Optional A over P Ref for ref(firstAoverP, withinAoverP) (For M=1, 2) (0.05, 0.01)
-MaxIter Optional MaxIteration for ref(For M=2) 10
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　


-mF details

Value Description
0 No CTF compensation
1 Phase only: W = CTF/|CTF|
2 Multiply  : W = CTF
3 Multiply  : W = 1/CTF
4 Wiener filter (constant noise): W = CTF/(|CTF|^2+N^2)
5 Multiply  : W = CTF^2


-mW details

Value Description
0 Weight = 1
1 Weight = (|in| + |ref|)/2


-mS details

Value Description
0 Sigma[Phase(i)]
1 Sigma[Phase(i)*Weight(i)] / Sigma[Weight(i)]


-mC details

Value Description
0 llExtractCtfinfFileCreate(m=0)'s format
1 llExtractCtfinfFileCreate(m=1)'s format


-M details

Value Description
0 CTF compensated single image
1 Three-dimentional reconstruction images that were made by nea and far Bessel separation.

CTF compensatation were done between min defocus to max defocus.
This mode is for myosin filaments.
(Options) -PixelSize, -Width, -truePitch, -dfRef, -AoverPRef, -MaxIter

-i, -r: It does not correspond to the file name too long.
2 Result FFT
(Options) -oF, -dfRef, -AoverPRef


Execution example

Input file's image

M=0 file(default)

Input-B120-CTF.png

Size

モード
Min
Max
Mean
SD

SE

( 80, 80, 1)

mrcComplexFloatFT
0.000514398 (78, 51, 0)
1684.3 (0, 0, 0)
9.67542
65.3969

0.817461


M=2 file
Input-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-298.592 (37, 36, 0)

46.4642 (56, 19, 0)
-21.0538
52.1224

0.65153


Reference file's image

M=0 file(default)

Input-B120-FFT.png

Size

Mode
Min
Max
Mean
SD

SE

( 80, 80, 1)

mrcComplexFloatFT
0.00776821 (75, 37, 0)
1684.3 (0, 0, 0)
9.41977
61.1799

0.764749


M=2 file
Input-B120.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

255 (49, 32, 0)
21.0538
47.6709

0.595886


Example of options only essential

-oP's image(z=0)
Outdata-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

0.0193939 (18, 72, 0)

2.0847 (13, 0, 0)
1.52075
0.209894

0.00147313
-o 's data
(18000.000000 0.720000): 0.019394
-oC 's data
       0.000000   -1 0
       0.042155   -1 0
       0.042155    0 0


Option -df

Case: df=(0, 27000, 200)

-oP 's image(z=0)
Outdata-df-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

0.0193939 (90, 72, 0)

2.11379 (68, 0, 0)
1.34909
0.459847

0.00392359
-o 's data
(17800.000000 0.830000): 0.019394
-oC 's data
       0.000000   -1 0
       0.041808   -1 0
       0.041808    0 0


In the following, Setting atdf=(0, 27000, 200)で実行

Option -kV

Case: kV=100

-oP 's image
Outdata-kV-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

0.0193939 (61, 75, 0)

2.09439 (46, 0, 0)
1.39997
0.391015

0.00333628
-o 's data
(12200.000000 0.750000): 0.019394
-oC 's data
       0.000000   -1 0
       0.042014   -1 0
       0.042014    0 0


Option -Cs

Case: Cs=1.7

-oP 's image
Outdata-Cs-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

0.0193939 (89, 82, 0)

2.13318 (68, 1, 0)
1.34903
0.459735

0.00392263
-o 's data
(17800.000000 0.820000): 0.019394
-oC 's data
       0.000000   -1 0
       0.041856   -1 0
       0.041856    0 0


Option -Ain

Case: Ain=0.1

-oP 's image
Outdata-Ain-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

0.0193939 (90, 72, 0)

2.11379 (68, 0, 0)
1.34909
0.459847

0.00392359
-o 's data
(17800.000000 0.830000): 0.019394
-oC 's data
       0.000000   -1 0
       0.041808   -1 0
       0.041808    0 0


Option -AoverP

Case: AoverP=(0.2, 0.8, 0.02)

-oP 's image
Outdata-AoverP-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

0.0193939 (90, 26, 0)

2.05561 (66, 0, 0)
1.34786
0.460559

0.00709308
-o 's data
(18000.000000 0.720000): 0.019394
-oC 's data
       0.000000   -1 0
       0.042155   -1 0
       0.042155    0 0


Option -Rmin, -Rmax

Case: Rmin=0.02, Rmax=0.08

-oP 's image
Outdata-RminRmax-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

6.98324e-07 (89, 96, 0)

2.35212 (50, 0, 0)
1.26243
0.571554

0.00487671
-o 's data
(17800.000000 0.959999): 0.000001
-oC 's data
       0.000000   -1 0
       0.041186   -1 0
       0.041186    0 0


Option -mF

Case: mF=0

-oP 's image
Outdata-M0-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

1.71139 (0, 0, 0)

1.71139 (0, 0, 0)
1.71139
9.28666e-07

7.92373e-09
-o 's data
(0.000000 0.000000): 1.711393
-oC 's data
       0.000000   -1 0
      -1.000000   -1 0
      -1.000000    0 0


Case: mF=3

-oP 's image
Outdata-mF3-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

1.43906e-06 (89, 96, 0)

2.16712 (66, 0, 0)
1.35241
0.46216

0.00394332
-o 's data
(17800.000000 0.959999): 0.000001
-oC 's data
       0.000000   -1 0
       0.041186   -1 0
       0.041186    0 0


Option -mC

mC=1

-oC 's data
   17800.000000        2.100000      200.000000        0.830000


Option -mW, -mS

Case: mW=1, mS=1

Case: No other settings
-oP 's image
Outdata-mWmS-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

0.00342354 (89, 96, 0)

2.48255 (0, 0, 0)
0.538199
0.224044

0.00191162
-o 's data
(17800.000000 0.959999): 0.003424
-oC 's data
       0.000000   -1 0
       0.041186   -1 0
       0.041186    0 0


Case: mF=2
-oP 's image
Outdata-mF2-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

0.00311023 (89, 100, 0)

2.42005 (0, 0, 0)
0.567162
0.258248

0.00220347
-o 's data
(17800.000000 0.999999): 0.003110
-oC 's data
       0.000000   -1 0
       0.041009   -1 0
       0.041009    0 0


Case: mF=4
-oP 's image
Outdata-mF4-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

0.00311023 (89, 100, 0)

2.42005 (0, 0, 0)
0.567162
0.258248

0.00220347
-o 's data
(17800.000000 0.999999): 0.003110
-oC 's data
       0.000000   -1 0
       0.041009   -1 0
       0.041009    0 0


Case: mF=5
-oP 's image
Outdata-mF5-mrcImageCTFDetermination.png

Min

Max
Mean
SD

SE

0.00279326 (89, 100, 0)

2.42334 (0, 0, 0)
0.586665
0.276375

0.00235814
-o 's data
(17800.000000 0.999999): 0.002793
-oC 's data
       0.000000   -1 0
       0.041009   -1 0
       0.041009    0 0


Option -M

Case: M=2

Case: No other settings
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