Difference between revisions of "mrcImageCTFObservation"

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'''mrcImageCTFObservation''' is [[Eos]]'s [[Command]] that [[mrcImage]]形式の画像に電子顕微鏡で撮影した際の画像変調をシミュレートするための
+
'''mrcImageCTFObservation''' is [[Eos]]'s [[Command]] for the simulated [[mrcImage]] in modulation when it is taken with an electron microscope. Output file can be used as an input file for the test of [[CTF Correction]].
  
 
== List of option ==
 
== List of option ==
Line 50: Line 50:
 
<td>-Ain</td>  
 
<td>-Ain</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>IlluminationAperture[mrad]</td>  
+
<td>IlluminationAperture[mrad] (when ctfMode=+32)</td>  
 
<td>0.0</td>  
 
<td>0.0</td>  
 
</tr>  
 
</tr>  
Line 73: Line 73:
 
<tr>  
 
<tr>  
 
<td>-Astig</td>  
 
<td>-Astig</td>  
−
<td>With Atigmatism</td>  
+
<td>Optional</td>  
−
<td>dfMin[A] dfMax[A] ASaxis[degree]</td>  
+
<td>With Atigmatism: dfMin[A] dfMax[A] ASaxis[degree]</td>  
 
<td>0 0 0</td>  
 
<td>0 0 0</td>  
 
</tr>  
 
</tr>  
Line 109: Line 109:
 
<tr>  
 
<tr>  
 
<td>+32</td>  
 
<td>+32</td>  
−
<td>With [[Illumination Angle]]</td>  
+
<td>With Illumination Angle</td>  
 
</tr>  
 
</tr>  
 
<tr>  
 
<tr>  
Line 117: Line 117:
 
</div>  
 
</div>  
 
</table>
 
</table>
−
 
  
 
== Execution example ==
 
== Execution example ==
−
===[[Media:Input-B120-CTF.mrc | Input file]] image===
+
===[[Media:Input-B120.mrc | Input file]] image===
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
−
<td>[[File:Input-mrcImageCTFObservation.png]]</td>  
+
<td>[[File:Input-B120.png]]</td>  
 
<td><p align="left">Min<br>  
 
<td><p align="left">Min<br>  
 
Max<br>  
 
Max<br>  
Line 130: Line 129:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-298.592 (37, 36, 0)<br>  
+
<td><p align="left">0 (0, 0, 0)<br>  
−
46.4642 (56, 19, 0)<br>  
+
255 (49, 32, 0)<br>  
−
-21.0538<br>  
+
21.0538<br>  
−
52.1224<br>  
+
47.6709<br>  
−
0.65153<br></p>  
+
0.595886<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 150: Line 149:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-66.9938 (29, 30, 0)<br>  
+
<td><p align="left">-73.5162 (35, 36, 0)<br>  
−
96.1484 (39, 34, 0)<br>  
+
57.3742 (50, 50, 0)<br>  
−
-1.94998e-08<br>  
+
3.09135e-08<br>  
−
18.286<br>  
+
14.5936<br>  
−
0.228575<br></p>  
+
0.18242<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
Line 161: Line 160:
  
 
=== Option -kV===
 
=== Option -kV===
−
====Mode: kV=100====  
+
====Case: kV=100====  
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
Line 171: Line 170:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-75.0422 (26, 28, 0)<br>  
+
<td><p align="left">-77.1076 (55, 33, 0)<br>  
−
102.125 (36, 34, 0)<br>  
+
65.1303 (29, 27, 0)<br>  
−
2.99404e-08<br>  
+
-9.05973e-09<br>  
−
20.3622<br>  
+
16.5308<br>  
−
0.254527<br></p>  
+
0.206634<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
=== Option -Cs===
 
=== Option -Cs===
−
====Mode: Cs=2====  
+
====Case: Cs=2====  
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
Line 192: Line 190:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-67.0312 (29, 30, 0)<br>  
+
<td><p align="left">-73.5104 (35, 36, 0)<br>  
−
96.1602 (39, 34, 0)<br>  
+
57.3753 (50, 50, 0)<br>  
−
1.87724e-08<br>  
+
-1.75032e-08<br>  
−
18.2861<br>  
+
14.5937<br>  
−
0.228576<br></p>  
+
0.182421<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
=== Option -df===
 
=== Option -df===
−
====Mode: df=54000====  
+
====Case: df=54000====  
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
Line 213: Line 210:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-75.6365 (29, 26, 0)<br>  
+
<td><p align="left">-73.2264 (52, 35, 0)<br>  
−
96.8578 (54, 34, 0)<br>  
+
61.0619 (26, 25, 0)<br>  
−
-5.46698e-09<br>  
+
5.85006e-08<br>  
−
21.2739<br>  
+
17.7402<br>  
−
0.265924<br></p>  
+
0.221752<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
=== Option -Astig===
 
=== Option -Astig===
Line 234: Line 230:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-62.1862 (59, 44, 0)<br>  
+
<td><p align="left">-56.8104 (43, 35, 0)<br>  
−
78.7101 (33, 53, 0)<br>  
+
57.875 (19, 31, 0)<br>  
−
-3.56755e-08<br>  
+
-2.03236e-09<br>  
−
18.5265<br>  
+
15.2833<br>  
−
0.231581<br></p>  
+
0.191041<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
=== Option -ctfMode===
 
=== Option -ctfMode===
Line 255: Line 250:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-66.9938 (29, 30, 0)<br>  
+
<td><p align="left">-73.5162 (35, 36, 0)<br>  
−
96.1484 (39, 34, 0)<br>  
+
57.3742 (50, 50, 0)<br>  
−
-1.94998e-08<br>  
+
-2.4918e-08<br>  
−
18.286<br>  
+
14.5936<br>  
−
0.228575<br></p>  
+
0.18242<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Mode: ctfMode=1, A=1====  
 
====Mode: ctfMode=1, A=1====  
Line 275: Line 269:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-62.9971 (27, 27, 0)<br>  
+
<td><p align="left">-261.062 (39, 38, 0)<br>  
−
310.586 (38, 36, 0)<br>  
+
47.4055 (28, 25, 0)<br>  
−
21.0538<br>  
+
-21.0538<br>  
−
58.8599<br>  
+
53.1561<br>  
−
0.735749<br></p>  
+
0.664451<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Mode: ctfMode=32====  
 
====Mode: ctfMode=32====  
Line 295: Line 288:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-66.9938 (29, 30, 0)<br>  
+
<td><p align="left">-73.5162 (35, 36, 0)<br>  
−
96.1484 (39, 34, 0)<br>  
+
57.3742 (50, 50, 0)<br>  
−
-1.94998e-08<br>  
+
1.68348e-08<br>  
−
18.286<br>  
+
14.5936<br>  
−
0.228575<br></p>  
+
0.18242<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Mode: ctfMode=32, Ain=0.1====  
 
====Mode: ctfMode=32, Ain=0.1====  
Line 323: Line 315:
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Mode: ctfMode=33, A=1, Ain=0.1====  
 
====Mode: ctfMode=33, A=1, Ain=0.1====  
Line 335: Line 326:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-56.019 (27, 27, 0)<br>  
+
<td><p align="left">-252.869 (39, 38, 0)<br>  
−
298.03 (38, 36, 0)<br>  
+
41.5229 (27, 26, 0)<br>  
−
21.0538<br>  
+
-21.0538<br>  
−
57.7534<br>  
+
52.1879<br>  
−
0.721917<br></p>  
+
0.652349<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Mode: ctfMode=256====  
 
====Mode: ctfMode=256====  
Line 355: Line 345:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-114.328 (37, 35, 0)<br>  
+
<td><p align="left">-50.3091 (27, 31, 0)<br>  
−
68.9204 (29, 28, 0)<br>  
+
82.1957 (55, 35, 0)<br>  
−
1.32575e-09<br>  
+
4.93391e-08<br>  
−
18.286<br>  
+
14.5936<br>  
−
0.228575<br></p>  
+
0.18242<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Mode: ctfMode=257, A=1====  
 
====Mode: ctfMode=257, A=1====  
Line 375: Line 364:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-317.886 (37, 36, 0)<br>  
+
<td><p align="left">-30.7261 (26, 25, 0)<br>  
−
73.1741 (29, 27, 0)<br>  
+
270.018 (36, 38, 0)<br>  
−
-21.0538<br>  
+
21.0538<br>  
−
58.8599<br>  
+
53.1561<br>  
−
0.735749<br></p>  
+
0.664451<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Mode: ctfMode=288, Ain=0.1====  
 
====Mode: ctfMode=288, Ain=0.1====  
Line 395: Line 383:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-99.5577 (37, 35, 0)<br>  
+
<td><p align="left">-45.6686 (27, 31, 0)<br>  
−
61.4533 (29, 28, 0)<br>  
+
65.0675 (55, 35, 0)<br>  
−
-5.21633e-08<br>  
+
2.81725e-08<br>  
−
16.94<br>  
+
13.2796<br>  
−
0.21175<br></p>  
+
0.165995<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Mode: ctfMode=289, A=1, Ain=0.1====  
 
====Mode: ctfMode=289, A=1, Ain=0.1====  
Line 415: Line 402:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">-299.98 (37, 36, 0)<br>  
+
<td><p align="left">-27.2028 (26, 26, 0)<br>  
−
56.6101 (29, 27, 0)<br>  
+
254.183 (36, 38, 0)<br>  
−
-21.0538<br>  
+
21.0538<br>  
−
57.7534<br>  
+
52.1879<br>  
−
0.721917<br></p>  
+
0.652349<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>

Latest revision as of 23:44, 17 September 2014

mrcImageCTFObservation is Eos's Command for the simulated mrcImage in modulation when it is taken with an electron microscope. Output file can be used as an input file for the test of CTF Correction.

List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: mrcImage NULL
-o Optional Output: mrcImage NULL
-kV Optional Acceleration voltage[kV] 200
-Cs Optional Spherical aberration coefficient[mm] 2.1
-df Optional Defocus (under is +) [A] 27000
-A Optional AmplitudeContrast/PhaseContrast(Amplitude/Phase) 0.0
-Ain Optional IlluminationAperture[mrad] (when ctfMode=+32) 0.0
-white Optional WhiteNoise(Noise/Signal) 1.0
-SinWin Optional RMin[A-1] RMax[A-1] 0.1 1.0
-ctfMode Optional ctfMode 0
-Astig Optional With Atigmatism: dfMin[A] dfMax[A] ASaxis[degree] 0 0 0
-c Optional configFile NULL
-m Optional mode 0

-ctfMode details

Value Description
0 Phase Only
1 Phase and Amplitude
+32 With Illumination Angle
+256 As Absolute Value

Execution example

Input file image

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

Outdata-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-73.5162 (35, 36, 0)

57.3742 (50, 50, 0)
3.09135e-08
14.5936

0.18242


Option -kV

Case: kV=100

Outdata-kV-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-77.1076 (55, 33, 0)

65.1303 (29, 27, 0)
-9.05973e-09
16.5308

0.206634

Option -Cs

Case: Cs=2

Outdata-Cs-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-73.5104 (35, 36, 0)

57.3753 (50, 50, 0)
-1.75032e-08
14.5937

0.182421

Option -df

Case: df=54000

Outdata-df-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-73.2264 (52, 35, 0)

61.0619 (26, 25, 0)
5.85006e-08
17.7402

0.221752

Option -Astig

Mode: Astig=(-54000, 54000, 45)

Outdata-Astig-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-56.8104 (43, 35, 0)

57.875 (19, 31, 0)
-2.03236e-09
15.2833

0.191041

Option -ctfMode

Mode: ctfMode=1

Outdata-ctfMode1-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-73.5162 (35, 36, 0)

57.3742 (50, 50, 0)
-2.4918e-08
14.5936

0.18242

Mode: ctfMode=1, A=1

Outdata-m1A-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-261.062 (39, 38, 0)

47.4055 (28, 25, 0)
-21.0538
53.1561

0.664451

Mode: ctfMode=32

Outdata-ctfMode32-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-73.5162 (35, 36, 0)

57.3742 (50, 50, 0)
1.68348e-08
14.5936

0.18242

Mode: ctfMode=32, Ain=0.1

Outdata-ctfMode32Ain-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-61.8551 (28, 30, 0)

85.9497 (38, 35, 0)
6.42321e-08
16.94

0.21175

Mode: ctfMode=33, A=1, Ain=0.1

Outdata-ctfMode33-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-252.869 (39, 38, 0)

41.5229 (27, 26, 0)
-21.0538
52.1879

0.652349

Mode: ctfMode=256

Outdata-ctfMode256-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-50.3091 (27, 31, 0)

82.1957 (55, 35, 0)
4.93391e-08
14.5936

0.18242

Mode: ctfMode=257, A=1

Outdata-ctfMode257-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-30.7261 (26, 25, 0)

270.018 (36, 38, 0)
21.0538
53.1561

0.664451

Mode: ctfMode=288, Ain=0.1

Outdata-ctfMode288-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-45.6686 (27, 31, 0)

65.0675 (55, 35, 0)
2.81725e-08
13.2796

0.165995

Mode: ctfMode=289, A=1, Ain=0.1

Outdata-ctfMode289-mrcImageCTFObservation.png

Min

Max
Mean
SD

SE

-27.2028 (26, 26, 0)

254.183 (36, 38, 0)
21.0538
52.1879

0.652349
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