Difference between revisions of "mrcImageCTFDetermination"

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'''mrcImageCTFDetermination''' is [[Eos]]'s [[Command]] for the estimation of the CTF。
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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 of [[ctfDisplay]].
  
  

Revision as of 07:29, 1 October 2014

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 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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