mrc2Dto3D - Revision history

Kinoshita: /* Euler Angle details */

2014-07-30T05:08:10Z

‎Euler Angle details

Kinoshita: /* Rotation Order details */

2014-07-30T05:07:50Z

‎Rotation Order details

Kinoshita: /* -i example */

2014-07-21T23:55:53Z

‎-i example

Kinoshita: /* -i example */

2014-07-15T02:42:12Z

‎-i example

Kinoshita: /* Main option */

2014-07-15T02:39:46Z

‎Main option

Kinoshita: /* Main option */

2014-07-15T02:21:53Z

‎Main option

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Kinoshita: Created page with "'''mrc2Dto3D''' is a command Eos to 3D images from 2D images which is an electron micrographs. From the angle information of the particle cut out, to r..."

2014-07-15T00:22:03Z

Created page with "'''mrc2Dto3D''' is a command Eos to 3D images from 2D images which is an electron micrographs. From the angle information of the particle cut out, to r..."

New page

'''mrc2Dto3D''' is a command Eos to [[3D images]] from [[2D images]] which is an [[electron micrographs]]. From the [[angle ]]information of the [[particle]] [[cut out]], to reconstruct a [[three-dimensional structure]] using a [[back projection technique]]. The output is a [[3d]] file [[dsn6]], it is possible to display (such as [[chimera]] or [[VMD]]) molecule viewer [[density map]].

== List of option ==

=== Main option ===

The setting of the mode and each parameter.

<table border=1>
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-i</td>
<td>Optional</td>
<td>Input: mrcImage[2DSet]</td>
<td>NULL</td>
</tr>
<tr>
<td>-I</td>
<td>Optional</td>
<td>InputDataFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-each</td>
<td>Optional</td>
<td>一つ一つのファイルを必要なときに読み込む</td>
<td></td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: mrcImage[3D]</td>
<td>NULL</td>
</tr>
<tr>
<td>-O</td>
<td>Optional</td>
<td>Output: </td>
<td>NULL</td>
</tr>
<tr>
<td>-single</td>
<td>Optional</td>
<td>傾斜軸を一つに設定</td>
<td>1</td>
</tr>
<tr>
<td>-InterpolationMode</td>
<td>Optional</td>
<td>展開モード</td>
<td>1</td>
</tr>
<tr>
<td>-Double</td>
<td>Optional</td>
<td>傾斜軸を２つに設定</td>
<td>　</td>
</tr>
<tr>
<td>-DoubleCounter</td>
<td>Optional</td>
<td>-Doubleを宣言した上で使用<br>
２つの傾斜軸を選択し、設定する</td>
<td>NULL</td>
</tr>
<tr>
<td>-CounterThreshold</td>
<td>Optional</td>
<td>-Doubleを宣言した上で使用<br>
波形の谷の閾値</td>
<td>1e-6</td>
</tr>
<tr>
<td>-CounterThresholdMode</td>
<td>Optional</td>
<td>-Doubleを宣言した上で使用<br>
波形の谷の閾値のモード</td>
<td>0</td>
</tr>
<tr>
<td>-WeightMode</td>
<td>Optional</td>
<td>-Doubleを宣言した上で使用<br>
重心のモード</td>
<td>0</td>
</tr>
<tr>
<td>-thicknessWeight</td>
<td>Optional</td>
<td>-Doubleを宣言した上で使用<br>
重心の深さ</td>
<td>　</td>
</tr>
<tr>
<td>-Sub</td>
<td>Optional</td>
<td>-Doubleを宣言した上で使用<br>
下位サンプリング</td>
<td>1</td>
</tr>
<tr>
<td>-PlusXrot</td>
<td>Optional</td>
<td>rasmolのためにｘ軸を180°回転</td>
<td>　</td>
</tr>
<tr>
<td>-SIRT</td>
<td>Optional</td>
<td>同時反復再構成法</td>
<td>　</td>
</tr>
<tr>
<td>-max</td>
<td>Optional</td>
<td>-SIRTを宣言した上で使用<br>
同時反復再構成法の最大値設定</td>
<td>30</td>
</tr>
<tr>
<td>-rms</td>
<td>Optional</td>
<td>-SIRTを宣言した上で使用<br>
同時反復再構成法の平方２乗平均を設定</td>
<td>1.0</td>
</tr>
<tr>
<td>-CTF</td>
<td>Optional</td>
<td>-SIRTを宣言した上で使用<br>
CTFInfoファイルを設定</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>

@@ Line 262: / Line 262: @@
 <br>
-=== [[Rotation Order|Euler Angle]] details ===
+=== [[Euler Angle|Rotation Order]] details ===
 <pre>
 st digit: Setting the rotation axis of the first

@@ Line 262: / Line 262: @@
 <br>
-=== [[Rotation Order]] details ===
+=== [[Rotation Order|Euler Angle]] details ===
 <pre>
 st digit: Setting the rotation axis of the first

@@ Line 300: / Line 300: @@
 File:121p.no2.out-In1-input1.png|Fig.1-1:XY-plane of the input image
 File:121p.no2.out-In1-input2.png|Fig.1-2:ZX-plane of the input image
-File:opution-i.png|Fig.2:Output
+File:opution-i.png|Fig.2:Output image
 </gallery>
 <br>

@@ Line 297: / Line 297: @@
   SE		9.13179e-06
 <gallery>
 File:121p.no2.out-In1-input1.png|Fig.1-1:XY-plane of the input image

@@ Line 29: / Line 29: @@
 				<td>-each</td>
 				<td>Optional</td>
-				<td>一つ一つのファイルを必要なときに読み込む</td>
+				<td>Read when needed files one by one</td>
 				<td></td>
 			</tr>