Difference between revisions of "mrcImageCTFCompensation"
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<td>-Cs</td> | <td>-Cs</td> | ||
<td>Optional</td> | <td>Optional</td> | ||
| − | <td>[[ | + | <td>[[Spherical aberration coefficient]][mm]</td> |
<td>2.1</td> | <td>2.1</td> | ||
</tr> | </tr> | ||
Revision as of 01:58, 18 July 2014
mrcImageCTFCompensation is Eos's Command that corrects CTF (Contrast transfer function) for mrcImage files taken by a transmission electron microscope.
Contents
- 1 List of option
- 2 Execution example
- 2.1 Input file image
- 2.2 -info data
- 2.3 -info2 のデータ
- 2.4 Example of options only essential
- 2.5 Option -m
List of option
Main option
| Option | Essential/Optional | Description | Default |
|---|---|---|---|
| -i | Essential | Input: mrcImage(FFT) | stdin |
| -o | Essential | Output: mrcImage | stdout |
| -info | Optional | CTF information: ASCII | NULL |
| -info2 | Optional | CTF information2: ASCII | NULL |
| -kV | Optional | Acceleration voltage[kV] | 200 |
| -Cs | Optional | Spherical aberration coefficient[mm] | 2.1 |
| -df | Optional | Defocus(under is +): [A] | 27000 |
| -white | Optional | WhiteNoise(Noise/Signal) | 0.1 |
| -SinWin | Optional | Windowing by sine function from Rmin[/A] to Rmax[/A].Default: No Window.: (SinWinRmin, SinWinRmax) | 補正なし |
| -A | Optional | The ratio of amplitude contrast to phase contrast(Amplitude/Phase) | 0.1 |
| -Astig | Optional | With Astigmatism (difMin, dfMax, asAxis)) | (0, 0 , 0) |
| -NoAstig | Optional | Without Astigmatism | |
| -c | Optional | ConfigurationFile | NULL |
| -m | Optional | Mode | 0 |
| -h | Optional | Help |
-m details
| Value | Description |
|---|---|
| 0 | No Correction |
| 1 | x ctf/|ctf| phase flipping |
| 2 | x ctf phase flipping and ctf-multiplying |
| 3 | x 1/ctf (0.1<|ctf| ) phase flipping and ctf-divided |
| 4 | x ctf/(SQR(ctf)+SQR(NS)) phase-flipping + Winner Filtering |
| 5 | x SQR(ctf) x ctf/|ctf| phase-flipping + ctf-Weighted |
| 6 | x 1/|ctf| (0.1<|ctf|) No phase-flipping + ctf-divided |
| 7 | x |ctf|/(SQR(ctf)+SQR(NS)) No phase flipping + Winner Filtering |
| 8 | x ctf /(SQR(ctf)+SQR(NS*exp(a*R))) phase flipping + Winner Filtering + NS-raising |
| 9 | x |ctf|/(SQR(ctf)+SQR(NS*exp(a*R))) No phase flipping + Winner Filtering + NS-raising |
-info format
defocus Cs kV AmplitudeContrast
-info2 format
Execution example
Input file image
 |
Min Max |
0.000514398 (78, 51, 0) 1684.3 (0, 0, 0) |
-info data
27000.000000 2.100000 200.000000 0.100000
-info2 のデータ
... ElaRShift: 0.25 flagAliasing: 1 9,NyquistFrequency: 0.2 ThonRingCanvas: 1 0,graph: .graph.graph0.graph InElaShift: 0.0108 defocus2D0: 27000 defocus2D1: 27000 ...
Example of options only essential
 |
Min Max |
-298.592 (37, 36, 0) 46.4642 (56, 19, 0) |
Option -m
Case: m=1, kV=200
Case: No other settings
 |
Min Max |
0 (0, 0, 0) 0 (0, 0, 0) |
Case: info=CTF information
 |
Min Max |
-38.9125 (41, 61, 0) 268.151 (39, 35, 0) |
Case: info2=CTF information2
 |
Min Max |
-38.9125 (41, 61, 0) 268.151 (39, 35, 0) |
Case: Cs=2.1
 |
Min Max |
-277.543 (37, 36, 0) 67.5181 (56, 19, 0) |
Case: df=27000
 |
Min Max |
-59.6211 (51, 54, 0) 244.573 (39, 35, 0) |
Case: A=0.1
 |
Min Max |
-46.4642 (56, 19, 0) 298.592 (37, 36, 0) |
Case: Astig=(2000, 3000, 30)
 |
Min Max |
-63.7102 (56, 19, 0) 278.233 (37, 35, 0) |
Case: m=2, info=CTF information
 |
Min Max |
-62.4959 (28, 30, 0) 115.688 (39, 34, 0) |
Case: m=3, info=CTF information
 |
Min Max |
-49.5112 (2, 15, 0) 1120.94 (39, 39, 0) |
Case: m=4, info=CTF information
Case: No other settings
 |
Min Max |
-76.6069 (1, 16, 0) 835.557 (40, 39, 0) |
Case: white=0.5
 |
Min Max |
-59.6252 (50, 54, 0) 195.105 (39, 35, 0) |
Case: m=5, info=CTF information
 |
Min Max |
-63.7521 (29, 30, 0) 81.6286 (39, 34, 0) |
Case: m=6, info=CTF information
 |
Min Max |
-1338.09 (37, 36, 0) 212.611 (2, 70, 0) |
Case: m=7, info=CTF information
Case: No other settings
 |
Min Max |
-885.311 (37, 36, 0) 43.1237 (2, 0, 0) |
Case: white=0.5
 |
Min Max |
-221.279 (37, 36, 0) 60.2085 (29, 27, 0) |
