Kinoshita: /* Rotation Order details */

2014-07-30T05:09:01Z

‎Rotation Order details

Kinoshita: /* Main option */

2014-07-30T05:08:43Z

‎Main option

Kinoshita: /* Option -EulerMode */

2014-07-16T04:15:59Z

‎Option -EulerMode

Kinoshita: /* Execution example */

2014-07-15T06:49:23Z

‎Execution example

Kinoshita: /* Execution example */

2014-07-15T06:48:50Z

‎Execution example

Kinoshita: /* Input file image */

2014-07-15T06:26:12Z

‎Input file image

Kinoshita: Created page with "'''mrc3Dto2D''' is Eos's Command that creates 2D Image from 3D Image. In this case, 3D image refers to the reference image mainly, 2D image refers ..."

2014-07-15T06:08:40Z

Created page with "'''mrc3Dto2D''' is Eos's Command that creates 2D Image from 3D Image. In this case, 3D image refers to the reference image mainly, 2D image refers ..."

New page

'''mrc3Dto2D''' is [[Eos]]'s [[Command]] that creates [[2D Image]] from [[3D Image]]. In this case, [[3D image]] refers to the [[reference image]] mainly, [[2D image]] refers to the [[projected image]] mainly. It is possible to acquire the [[projected image]] of the various [[angle]]s from the crystal structure (PDB file) or similar structure. [[Projected image]] output is used to [[determine]] the [[angle]] of the particles in a [[single particle analysis]].

== 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>-i</td>
<td>Essential</td>
<td>Input: [[mrcImage]](3D)</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[mrcImage]](2DSet)</td>
<td>NULL</td>
</tr>
<tr>
<td>-Rot1</td>
<td>Optional</td>
<td>1st Rotation</td>
<td>0.0 360.0 10</td>
</tr>
<tr>
<td>-Rot2</td>
<td>Optional</td>
<td>2nd Rotaion</td>
<td>0.0 360.0 10</td>
</tr>
<tr>
<td>-Rot3</td>
<td>Optional</td>
<td>Last Rotaion</td>
<td>0.0 360.0 10</td>
</tr>
<tr>
<td>-EulerMode</td>
<td>Optional</td>
<td>Rotaion mode of [[Euler angle]]</td>
<td>ZOYS</td>
</tr>
<tr>
<td>-InterpolationMode</td>
<td>Optional</td>
<td>[[Interpolation mode]]</td>
<td>1</td>
</tr>
<tr>
<td>-AreaMode</td>
<td>Optional</td>
<td>AreaMode：Form of the whole space to be projected<br>
0: square 1: sphere</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>
<br>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Projection by the number of all.</td>
</tr>
<tr>
<td>1</td>
<td>Reducing the number of projections in accordance with the rotation angle.<br>
Axis nRot3=1 and Rot2 if is perpendicular to the 2D image plane, it is possible to reduce the number of projections.</td>
</tr>
</table>
<br>

=== -InterpolationMode details ===
Setting of [[Interpolation Mode]].
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Nearest neighbor method</td>
</tr>
<tr>
<td>1</td>
<td>Bi-linear interpolation method</td>
</tr>
<tr>
<td>2</td>
<td>Cubic convolution method</td>
</tr>
<tr>
<td>3</td>
<td>Polynomial interpolation method</td>
</tr>
</table>
<br>

=== [[Rotation Order]] details ===
<pre>
1st digit: Setting the rotation axis of the first
2nd digit: Setting the order-1 of the rotation axis
O: Order Z -> Y-> X
E: Order Z -> X-> Y
3rd digit: Setting the order-2 of the rotation axis
Y: Keep the order
N: Reverse the order
4th digit: Setting rotation method
S: Rotate the object
N: Move the coordinates
</pre>
<br>

== Execution example ==
===Input file image===
[[File:121p.png]]

Details of the input file as seen by [[pdbInfo]].

[[File:121p-Info.png]]

Converting to [[mrcImage]] file(3D) by [[pdb2mrc]].
<table>
<tr>
<td>XY-plane</td>
<td>YZ-plane</td>
</tr>
<tr>
<td>[[File:121p.mrc.png]]</td>
<td>[[File:121p.mrc-2.png]]</td>
</tr>
</table>
<br>

=== Example of options only essential ===
<table>
<tr>
<td>[[File:121p.no2.out-m0.png]]</td>
<td>Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
</td>
<td>0<br>
0.186008<br>
0.00302756<br>
0.0128325<br>
7.12722e-07<br>
</td>
</tr>
</table>
<br>

===Option -Rot1 -Rot2 -Rot3===

<div>Setting at 0 180 30 to Rot of all.<br>
</div>
<table>
<tr>
<td>XY-plane</td>
<td>YZ-plane</td>
</tr>
<tr>
<td>[[File:121p.no2.out-Rot-2.png]]</td>
<td>[[File:121p.no2.out-Rot-1.png]]</td>
<td>Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
</td>
<td>0<br>
0.175<br>
0.00302838<br>
0.0129759<br>
8.75794e-06<br>
</td>
</tr>
</table>
<br>

===Option -EulerMode===

<div>Setting at 0 180 30 to Rot of all, and setting at EOYS to EulerMode.<br>
</div>
<table>
<tr>
<td>XY-plane</td>
<td>YZ-plane</td>
</tr>
<tr>
<td>[[File:121p.no2.out-Rot-EY2.png]]</td>
<td>[[File:121p.no2.out-Rot-EY.png]]</td>
<td>Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
</td>
<td>0<br>
0.175<br>
0.00303008<br>
0.0129694<br>
8.75351e-06<br>
</td>
</tr>
</table>
<br>

<div>Setting at 0 180 30 to Rot of all later.</div>
<br>

===Option -InterpolationMode===
====InterpolationMode: 0====
<table>
<tr>
<td>[[File:121p.no2.out-In0.png]]</td>
<td>Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
</td>
<td>0<br>
0.2125<br>
0.00301082<br>
0.0137354<br>
9.27052e-06<br>
</td>
</tr>
</table>
<br>

====InterpolationMode: １====
<table>
<tr>
<td>[[File:121p.no2.out-In1.mrc.png]]</td>
<td>Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
</td>
<td>0<br>
0.175<br>
0.00302838<br>
0.0129759<br>
8.75794e-06<br>
</td>
</tr>
</table>
<div>There is no change in the image so the mode is 1 by default.</div>
<br>

====InterpolationMode: 2====
<table>
<tr>
<td>[[File:121p.no2.out-In2.png]]</td>
<td>Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
</td>
<td>-0.0325619<br>
0.213961<br>
0.00302793<br>
0.0137247<br>
9.26332e-06<br>
</td>
</tr>
</table>
<br>

====InterpolationMode: 3====
<table>
<tr>
<td>[[File:121p.no2.out-In3.png]]</td>
<td>Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
</td>
<td>-5.4667<br>
184.383<br>
3.28548<br>
13.7206<br>
0.00926055<br>
</td>
</tr>
</table>

@@ Line 238: / Line 238: @@
 <br>
-<div>Setting at 0 180 30 to Rot of all later.</div>
+<div>In the following, Setting at 0 180 30 to Rot of all.</div>
 <br>

@@ Line 140: / Line 140: @@
 == Execution example ==
-===Image of Input file===
+===Input file's image===
 	[[File:121p.png]]

← Older revision		Revision as of 06:26, 15 July 2014
Line 144:		Line 144:


−	Details of the input file ~~as seen~~ by [[pdbInfo]].	+	Details for the input file by [[pdbInfo]].

	[[File:121p-Info.png]]		[[File:121p-Info.png]]

@@ Line 124: / Line 124: @@
 <br>
-=== [[Rotation Order]] details ===
+=== [[Euler Angle|Rotation Order]] details ===
 <pre>
 st digit: Setting the rotation axis of the first

@@ Line 43: / Line 43: @@
 			<td>-EulerMode</td>
 			<td>Optional</td>
-			<td>Rotaion mode of [[Euler angle]]</td>
+			<td>Rotaion mode of [[Euler Angle]]</td>
 			<td>ZOYS</td>
 		</tr>
@@ Line 79: / Line 79: @@
 	</table>
 <br>
-−
 === -m details ===
 	<table border="1">

mrc3Dto2D - Revision history

Kinoshita: /* Rotation Order details */

Kinoshita: /* Main option */

Kinoshita: /* Option -EulerMode */

Kinoshita: /* Execution example */

Kinoshita: /* Execution example */

Kinoshita: /* Input file image */

Kinoshita: Created page with "'''mrc3Dto2D''' is Eos's Command that creates 2D Image from 3D Image. In this case, 3D image refers to the reference image mainly, 2D image refers ..."