Difference between revisions of "mrcImageCTFObservation"

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'''mrcImageCTFObservation''' is [[Eos]]'s [[Command]] for the simulated [[mrcImage]] in modulation when it is taken with an electron microscope.
+
'''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 160: Line 160:
  
 
=== Option -kV===
 
=== Option -kV===
−
====Mode: kV=100====  
+
====Case: kV=100====  
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
Line 170: 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 191: 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 212: 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 233: 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 254: 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 274: 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 294: 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 322: Line 315:
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
  
 
====Mode: ctfMode=33, A=1, Ain=0.1====  
 
====Mode: ctfMode=33, A=1, Ain=0.1====  
Line 334: 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 354: 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 374: 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 394: 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 414: 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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