defocusDeterminationFromThonRing
From EosPedia
defocusDeterminationFromThonRing is Eos's Command.
Contents
List of option
Main option
| Option | Essential/Optional | Description | Default |
|---|---|---|---|
| -i | Optional | Input | stdin |
| -iN | Optional | InputNameInInformationFile | stdin |
| -iR | Optional | InputReferenceForLength: mrcImage | stdin |
| -o | Optional | Output: ASCII | stdout |
| -oI | Optional | OutputInformationFile1: ASCII(mrcImageMultiCTFCompensation and mrcImageCTFCompensation) | stdout |
| -oI2 | Optional | OutputInformationFile2: ASCII(llDataCTFCompensate -I2) | stdout |
| -oI3 | Optional | OutputInformationFile3: ASCII(llExtractWithLayerSeparation) Options: -truePitch, -PixelSize, -deltadY and -ctfMode |
stdout |
| -kV | Optional | Acceleration voltage: [kV] | 200 |
| -Cs | Optional | Spherical aberration coefficient: [mm] | 2.1 |
| -A | Optional | The ratio of amplitude contrast to phase contrast | 0.05 |
| -truePitch | Optional | True Pitch | 430 |
| -PixelSize | Optional | Pixel Size [A] | 5 |
| -deltadY | Optional | A range of deltadY to determine dY. | 0.5 |
| -R | Optional | Variable: Thon Ring: [/A] | NULL ... |
| -c | Optional | ConfigurationFile | NULL |
| -m | Optional | Mode | 0 |
| -ctfMode | Optional | CTFMode | 0 |
| -h | Optional | Help |
-m details
| Value | Description |
|---|---|
| 0 |
CTFMode details
| Value | Description |
|---|---|
| 0 | Phase CTF |
| 1 | PhaseCTF + ratio*AmpCTF |
Execution example
Case: Options only essential
>>> Underfocus Ring Number Amount of defocus[A] R[1/A] --------------------------------------------- Avg. nan [A] +- S.D. nan [A] Avg. nan [um] +- S.D. nan [um] >>> Overfocus Ring Number Amount of defocus[A] R[1/A] --------------------------------------------- Avg. nan [A] +- S.D. nan [A] Avg. nan [um] +- S.D. nan [um]
Option -R
Case: R=(0.001, 0.01, 0.1)
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196908e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335249e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196396e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891301e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
Option -o, -oI, -oI2
Case: o, oI, oI2 specify file, R=(0.001, 0.01, 0.1)
-o 's data
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196908e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335249e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196396e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891301e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
-oI 's data
stdin 13352487.000000 2.100000 200.000000 0.050000
-oI2 's data
13352487.000000 2.100000 200.000000 0.050000
Option -iR
Case: -iR specify file, R=(0.001, 0.01, 0.1)
-iR image
 |
Min Max |
0 (0, 0, 0) 255 (49, 32, 0) |
Case: -oI3 specify file
Output
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196908e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335249e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196396e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891301e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
LengthY 400.000000 [A] = LengthY 80 [Pixel] x PixelSize 5.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY 0.930233
CalculatedY 1.000000
deltadY 0.069767
-oI3 data
stdin 1 13352487.000000 2.100000 200.000000 0.050000 0
Case: truePitch=300
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196908e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335249e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196396e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891301e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
LengthY 400.000000 [A] = LengthY 80 [Pixel] x PixelSize 5.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY 1.333333
CalculatedY 1.000000
deltadY 0.333333
Case: PixelSize=10
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196908e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335249e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196396e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891301e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
LengthY 800.000000 [A] = LengthY 80 [Pixel] x PixelSize 10.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY 1.860465
CalculatedY 2.000000
deltadY 0.139535
Option -kV
Case: kV=100, R=(0.001, 0.01, 0.1)
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 2.659654e+07 : 1.000000e-03
2 5.362301e+05 : 1.000000e-02
3 8.208672e+03 : 1.000000e-01
---------------------------------------------
Avg. 9.046993e+06 [A] +- S.D. 1.241128e+07 [A]
Avg. 904.70 [um] +- S.D. 1241.13 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -2.745611e+07 : 1.000000e-03
-2 -5.448229e+05 : 1.000000e-02
-3 -8.007123e+03 : 1.000000e-01
---------------------------------------------
Avg. -9.336313e+06 [A] +- S.D. 1.281450e+07 [A]
Avg. -933.63 [um] +- S.D. 1281.45 [um]
Option -Cs
Case: Cs=2.0, R=(0.001, 0.01, 0.1)
Output
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196594e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335248e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196710e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891300e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
-oI 's data
stdin 13352485.000000 2.000000 200.000000 0.050000
Option -A
Case: A=0.1, R=(0.001, 0.01, 0.1)
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.862291e+07 : 1.000000e-03
2 7.851137e+05 : 1.000000e-02
3 1.190596e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.313998e+07 [A] +- S.D. 1.802192e+07 [A]
Avg. 1314.00 [um] +- S.D. 1802.19 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.115387e+07 : 1.000000e-03
-2 -8.104219e+05 : 1.000000e-02
-3 -1.202707e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.399211e+07 [A] +- S.D. 1.920903e+07 [A]
Avg. -1399.21 [um] +- S.D. 1920.90 [um]
