ctfZeroPoint - Revision history

Kinoshita: Created page with "'''ctfZeroPoint''' is Eos's Command. == List of option == === Main option === ..."
2014-08-20T01:11:14Z
Created page with "'''ctfZeroPoint''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optional</th>..."
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'''ctfZeroPoint''' is [[Eos]]'s [[Command]].

== List of option ==
=== Main option ===
<table border="1">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: [[ASCII]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-RMax</td>
<td>Optional</td>
<td>max Spatial frequency[/A]</td>
<td>0.1</td>
</tr>
<tr>
<td>-dR</td>
<td>Optional</td>
<td>delta Spatial frequency[/A]</td>
<td>0.0001</td>
</tr>
<tr>
<td>-kV</td>
<td>Optional</td>
<td>[[Acceleration voltage]][kV]</td>
<td>200</td>
</tr>
<tr>
<td>-Cs</td>
<td>Optional</td>
<td>[[Spherical aberration coefficient]][mm]</td>
<td>2.1</td>
</tr>
<tr>
<td>-df</td>
<td>Optional</td>
<td>defocus: [A]:under(+)</td>
<td>27000</td>
</tr>
<tr>
<td>-dfMin</td>
<td>Optional</td>
<td>min defocus: [A]</td>
<td>0</td>
</tr>
<tr>
<td>-dfMax</td>
<td>Optional</td>
<td>max defocus: [A]</td>
<td>200000</td>
</tr>
<tr>
<td>-deltadf</td>
<td>Optional</td>
<td>delta defocus[A]</td>
<td>2000</td>
</tr>
<tr>
<td>-A</td>
<td>Optional</td>
<td>AmplitudeContrast/PhaseContrast</td>
<td>0.05</td>
</tr>
<tr>
<td>-N</td>
<td>Optional</td>
<td>Ordinal number of zero point</td>
<td>1.0</td>
</tr>
<tr>
<td>-Ain</td>
<td>Optional</td>
<td>[[Illumination Aperture]][mrad]</td>
<td>0.02</td>
</tr>
<tr>
<td>-ctfMode</td>
<td>Optional</td>
<td>CTFMode</td>
<td>0</td>
</tr>
<tr>
<td>-c</td>
<td>Optional</td>
<td>ConfigurationFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Mode</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>One zero point</td>
</tr>
<tr>
<td>1</td>
<td>All zero points </td>
</tr>
<tr>
<td>2</td>
<td>All zero points along defocus </td>
</tr>
</table>

===CTFMode details===
<table border="1">
<div align="left">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Phase CTF</td>
</tr>
<tr>
<td>1</td>
<td>PhaseCTF + ratio*AmpCTF </td>
</tr>
</div>
</table>

== Execution example ==
=== Case: Options only essential ===
<pre>
[ZeroPointResult] AmpContrast 0.050000
Amount of Defocus [A] Number R [A] .........
27000.000000 1 0.038443
</pre>

=== Option -kV===
====Case: kV=100====
<pre>
[ZeroPointResult] AmpContrast 0.050000
Amount of Defocus [A] Number R [A] .........
27000.000000 1 0.031647
</pre>

=== Option -Cs===
====Case: Cs=5.0====
<pre>
[ZeroPointResult] AmpContrast 0.050000
Amount of Defocus [A] Number R [A] .........
27000.000000 1 0.038453
</pre>

=== Option -df===
====Case: df=20000====
<pre>
[ZeroPointResult] AmpContrast 0.050000
Amount of Defocus [A] Number R [A] .........
20000.000000 1 0.044674
</pre>

=== Option -A===
====Case: A=0.1====
<pre>
[ZeroPointResult] AmpContrast 0.100000
Amount of Defocus [A] Number R [A] .........
27000.000000 1 0.038443
</pre>

=== Option -N===
====Case: N=2====
<pre>
[ZeroPointResult] AmpContrast 0.050000
Amount of Defocus [A] Number R [A] .........
27000.000000 2 0.054377
</pre>

=== Option -ctfMode===
====Case: ctfMode=1====
<pre>
[ZeroPointResult] AmpContrast 0.050000
Amount of Defocus [A] Number R [A] .........
27000.000000 1 0.038136
</pre>

=== Option -m===
====Case: m=1, N=2====
<pre>
[ZeroPointResult] AmpContrast 0.050000
Amount of Defocus [A] Number R [A] .........
27000.000000 2 0.038443 0.054377
</pre>

====Case: m=2====
=====Case: No other settings=====
<pre>
[ZeroPointResult] AmpContrast 0.050000
Amount of Defocus [A] Number R [A] .........
0.000000 1 -1.000000
2000.000000 1 -1.000000
4000.000000 1 -1.000000
6000.000000 1 0.081838
8000.000000 1 0.070758
10000.000000 1 0.063241
12000.000000 1 0.057707
14000.000000 1 0.053414
16000.000000 1 0.049956

...

80000.000000 1 0.022330
82000.000000 1 0.022056
84000.000000 1 0.021792
86000.000000 1 0.021537
88000.000000 1 0.021291
90000.000000 1 0.021053
92000.000000 1 0.020823
94000.000000 1 0.020600
96000.000000 1 0.020384
98000.000000 1 0.020175
100000.000000 1 0.019972

...

190000.000000 1 0.014489
192000.000000 1 0.014414
194000.000000 1 0.014339
196000.000000 1 0.014266
198000.000000 1 0.014194
200000.000000 1 0.014122
</pre>

=====Case: dfMin=8000, dfMax=100000, deltadf=4000=====
<pre>
[ZeroPointResult] AmpContrast 0.050000
Amount of Defocus [A] Number R [A] .........
8000.000000 1 0.070758
12000.000000 1 0.057707
16000.000000 1 0.049956
20000.000000 1 0.044674
24000.000000 1 0.040777
28000.000000 1 0.037750
32000.000000 1 0.035311
36000.000000 1 0.033290
40000.000000 1 0.031581
44000.000000 1 0.030111
48000.000000 1 0.028829
52000.000000 1 0.027698
56000.000000 1 0.026690
60000.000000 1 0.025785
64000.000000 1 0.024966
68000.000000 1 0.024220
72000.000000 1 0.023538
76000.000000 1 0.022910
80000.000000 1 0.022330
84000.000000 1 0.021792
88000.000000 1 0.021291
92000.000000 1 0.020823
96000.000000 1 0.020384
100000.000000 1 0.019972
</pre>

Option Essential/Optional