pdb2mrc2d - Revision history

Kinoshita: /* Execution example */

2014-08-07T04:08:59Z

‎Execution example

Kinoshita: /* Option -S */

2014-08-07T04:03:48Z

‎Option -S

Kinoshita: /* Option -Rot */

2014-08-07T04:03:32Z

‎Option -Rot

Kinoshita: /* Output file→3D */

2014-08-07T04:01:12Z

‎Output file→3D

Kinoshita: /* Execution example */

2014-08-07T03:09:41Z

‎Execution example

Kinoshita: /* RotModeの設定 details */

2014-08-07T03:08:17Z

‎RotModeの設定 details

Kinoshita: /* -m details */

2014-08-07T03:00:05Z

‎-m details

Kinoshita: /* Main option */

2014-08-07T02:50:34Z

‎Main option

Kinoshita at 02:43, 7 August 2014

2014-08-07T02:43:20Z

Kinoshita: Created page with "'''pdb2mrc2d'''はpdbfileをmrcImagefileに変換する Eos's Command. == List of option == === Main option ===

..."
2014-08-07T02:41:16Z
Created page with "'''pdb2mrc2d'''はpdbfileをmrcImagefileに変換する Eos's Command. == List of option == === Main option === <table border="1"> <div align="left"> <tr>..."
New page
'''pdb2mrc2d'''はpdbfileを[[mrcImage]]fileに変換する [[Eos]]'s [[Command]].

== List of option ==
=== Main option ===
<table border="1">
<div align="left">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-i</td>
<td>Essential</td>
<td>Input設定: [[PDB]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output設定: [[mrcImage]](2D)</td>
<td>NULL</td>
</tr>
<tr>
<td>-O</td>
<td>Optional</td>
<td>Output設定: [[mrcImage]](3D)</td>
<td>NULL</td>
</tr>
<tr>
<td>-d</td>
<td>Essential</td>
<td>1ピクセルのWidthを指定</td>
<td>5.0 5.0</td>
</tr>
<tr>
<td>-s</td>
<td>Optional</td>
<td>画像の位置を指定</td>
<td>0.0 0.0</td>
</tr>
<tr>
<td>-n</td>
<td>Essential</td>
<td>画像のサイズを指定</td>
<td>0 0</td>
</tr>
<tr>
<td>-Rot</td>
<td>Optional</td>
<td>回転（ｘ軸、ｙ軸のみ）</td>
<td>1 1</td>
</tr>
<tr>
<td>-S</td>
<td>Optional</td>
<td>Z軸→X軸→Y軸の順で回転</td>
<td>0.0 0.0 0.0</td>
</tr>
<tr>
<td>-startEA</td>
<td>Optional</td>
<td>[[Euler Angle]]を設定</td>
<td>YOYS 0.0 0.0 0.0</td>
</tr>
<tr>
<td>-EAMode</td>
<td>Optional</td>
<td>RotationModeを指定</td>
<td>YOYS</td>
</tr>
<tr>
<td>-EARot1</td>
<td>Optional</td>
<td>主となる回転</td>
<td>5.0 0.0 180.0</td>
</tr>
<tr>
<td>-EARot2</td>
<td>Optional</td>
<td>-EARot1とは別の回転</td>
<td>5.0 0.0 180.0</td>
</tr>
<tr>
<td>-w</td>
<td>Optional</td>
<td>重量を設定</td>
<td>1.0</td>
</tr>
<tr>
<td>-sig</td>
<td>Optional</td>
<td>原子の半径を指定</td>
<td>0.0</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Mode設定</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</div>
</table>

=== -m details ===
<table border="1">
<div align="left">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>メルカトール図法・等角</td>
</tr>
<tr>
<td>1</td>
<td>モルワイデ図法・等角</td>
</tr>
<tr>
<td>2</td>
<td>メルカトール図法・等積</td>
</tr>
<tr>
<td>3</td>
<td>モルワイデ図法・等積</td>
</tr>
</div>
</table>
<br>
<br>
<div>※Case: -Sと-startEAの両方が宣言されていた場合、-Sを実行した後に-startEAが実行される<br>
※軸を中心にもってきたい場合は、pdbInfoで軸を調べ、pdbMoveで軸の＋とーを逆にして実行する</div>

===RotModeの設定 details===
<table>
<tr>
<td>一桁目:</td>
<td>どの軸から回転を始めるか設定</td>
</tr>
<tr>
<td>二桁目:</td>
<td>回転軸の順番を設定１</td>
</tr>
<tr>
<td></td>
<td>O…Z→Y→Xの順に回転軸を変更する<br>
E…Z→X→Yの順に回転軸を変更する</td>
</tr>
<tr>
<td>三桁目:</td>
<td>回転軸の順番の設定２</td>
</tr>
<tr>
<td></td>
<td>Y…順番を維持する<br>
N…順番を逆順にする</td>
</tr>
<tr>
<td>四桁目:</td>
<td>回転方法を設定</td>
</tr>
<tr>
<td></td>
<td>Y…物体そのものをまわす<br>
D…座標を移動させる</td>
</tr>
</table>

== Execution example ==
===[[:Media:Input-121P-Move.pdb.zip|Input file]] image===
<div>[[File:121p-move-pdb2mrc2d.png]]<br>
pdbInfoでみたInput fileの詳細<br>
[[File:121p-move-info-pdb2mrc2d.png]]<br></div>
<br>

===Output file image===
<div>Optionを使用し、画像に物体が写るよう調整する<br>
今回のInput fileでは下記のようにOptionを設定すると、物体がほぼ中心に写る<br></div>

<table border="1">
<tr>
<td>-d</td>
<td>0.8 0.8</td>
</tr>
<tr>
<td>-s</td>
<td>-40 -40</td>
</tr>
<tr>
<td>-n</td>
<td>100 100</td>
</tr>
</table>
<br>

====Output file→2D====
[[File:121p.2d-pdb2mrc2d.png]]

====Output file→3D<br>====
[[File:121p.3d-pdb2mrc2d.png]]<br>
<div>このOptionを使用した場合、二つ's imageに相違点はない</div>
<br>

=== Option -Rot===
====-Rot 6 6に設定====
=====Output file→2D=====
[[File:121p.2d-Rot-pdb2mrc2d.png]]

=====Output file→3D（2Dの結果を繋ぎ、3Dで出力している）=====
<table>
<tr>
<td>ｘｙ平面の図</td>
<td>ｙｚ平面の図</td>
</tr>
<tr>
<td>[[File:121p.3d-EAMode1-pdb2mrc2d.png]]</td>
<td>[[File:121p.3d-EAMode2-pdb2mrc2d.png]]</td>
</tr>
</table>
<br>

=== Option -S===
====-Rot 6 6、-S 30 30 30に設定====
=====Output file→2D=====
[[File:121p.2d-S30-pdb2mrc2d.png]]
<br>

=== Option -startEA===
====-Rot 6 6、-startEA XOYS 30 30 30に設定====
=====Output file→2D=====
[[File:121p.2d-startEA30-pdb2mrc2d.png]]
<br>

=== Option -EAMode===
====-Rot 6 6、-EAMode XOYSに設定====
=====Output file→2D=====
[[File:121p.2d-EAMove-pdb2mrc2d.png]]
<br>

====-Rot 6 6、-EAMode YOYSに設定====
=====Output file→2D=====
[[File:121p.2d-EAModeY-pdb2mrc2d.png]]
<br>

=== Option -EARot1,-EARot2===
====-EARot1 10 20 70,-EARot2 20 50 100に設定====
=====Output file→2D=====
[[File:121p.2d-EARot12-pdb2mrc2d.png]]
<br>

=== Option -sig===
====-sig 1に設定、Output fileは-oとする====
[[File:121p.2d-sig-pdb2mrc2d.png]]
<br>

=== Option -w===
====-w 10に設定、Output fileは-oとする====
====-wを指定しなかった場合's imagedata====
[[File:121p.2d-w1-pdb2mrc2d.png]]
<br>

====-w 10を指定した場合's imagedata====
[[File:121p.2d-w2-pdb2mrc2d.png]]
<br>

=== Option -m===
<table>
<tr>
<td>Case: m=0</td>
</tr>
<tr>
<td>[[File:121p.2d-pdb2mrc2d.png]]</td>
<td>[[File:m0-pdb2mrc2d.png]]</td>
</tr>
<tr>
<td>Case: m=1</td>
</tr>
<tr>
<td>[[File:121p.2d-m1-pdb2mrc2d.png]]</td>
<td>[[File:m1-pdb2mrc2d.png]]</td>
</tr>
<tr>
<td>Case: m=2</td>
</tr>
<tr>
<td>[[File:121p.2d-m2-pdb2mrc2d.png]]</td>
<td>[[File:m2-pdb2mrc2d.png]]</td>
</tr>
<tr>
<td>Case: m=3</td>
</tr>
<tr>
<td>[[File:121p.2d-m3-pdb2mrc2d.png]]</td>
<td>[[File:m3-pdb2mrc2d.png]]</td>
</tr>

</table>
<div>今回's imageでは変化がわかりづらいが、画像dataの詳細を見ると、変化があることが分かる</div>

← Older revision		Revision as of 02:43, 7 August 2014
Line 1:		Line 1:
−	'''pdb2mrc2d'''~~はpdbfileを[[mrcImage]]fileに変換する~~ [[Eos]]'s [[Command]].	+	'''pdb2mrc2d''' [[Eos]]'s [[Command]] that converts from [[PDB]] file to [[mrcImage]] file.

	== List of option ==		== List of option ==

@@ Line 235: / Line 235: @@
 === Option -startEA===
-====-Rot 6 6、-startEA XOYS 30 30 30に設定====
+====Case: -Rot 6 6、-startEA XOYS 30 30 30====
 =====Output file→2D=====
 	[[File:121p.2d-startEA30-pdb2mrc2d.png]]
@@ Line 241: / Line 241: @@
 === Option -EAMode===
-====-Rot 6 6、-EAMode XOYSに設定====
+====Case: -Rot 6 6、-EAMode XOYS====
 =====Output file→2D=====
 	[[File:121p.2d-EAMove-pdb2mrc2d.png]]
 <br>
-====-Rot 6 6、-EAMode YOYSに設定====
+====Case: -Rot 6 6、-EAMode YOYS====
 =====Output file→2D=====
 	[[File:121p.2d-EAModeY-pdb2mrc2d.png]]
@@ Line 252: / Line 252: @@
 === Option -EARot1,-EARot2===
-====-EARot1 10 20 70,-EARot2 20 50 100に設定====
+====Case: -EARot1 10 20 70,-EARot2 20 50 100====
 =====Output file→2D=====
 	[[File:121p.2d-EARot12-pdb2mrc2d.png]]
@@ Line 258: / Line 258: @@
 === Option -sig===
-====-sig 1に設定、Output fileは-oとする====
+====Case: -sig 1, Output file is -o====
 	[[File:121p.2d-sig-pdb2mrc2d.png]]
 <br>
 === Option -w===
-====-w 10に設定、Output fileは-oとする====
+====Case: -w 10, Output file is -o====
-====-wを指定しなかった場合's imagedata====
+====without -w image data====
 	[[File:121p.2d-w1-pdb2mrc2d.png]]
 <br>
-====-w 10を指定した場合's imagedata====
+====-w 10 image data====
 	[[File:121p.2d-w2-pdb2mrc2d.png]]
 <br>
@@ Line 304: / Line 304: @@
 	</table>
-	<div>今回's imageでは変化がわかりづらいが、画像dataの詳細を見ると、変化があることが分かる</div>
+	<div>In this time, It is not easy to see these difference. But, you can see it by image data details.</div>

@@ Line 229: / Line 229: @@
 === Option -S===
-====-Rot 6 6、-S 30 30 30に設定====
+====Case: -Rot 6 6、-S 30 30 30====
 =====Output file→2D=====
 	[[File:121p.2d-S30-pdb2mrc2d.png]]

@@ Line 211: / Line 211: @@
 === Option -Rot===
-====-Rot 6 6に設定====
+====Case: -Rot 6 6====
 =====Output file→2D=====
 	[[File:121p.2d-Rot-pdb2mrc2d.png]]
-=====Output file→3D（2Dの結果を繋ぎ、3Dで出力している）=====
+=====Output file→3D(Display at 3D by combining 2D result.)=====
 	<table>
 		<tr>
-			<td>ｘｙ平面の図</td>
+			<td>xy-plane</td>
-			<td>ｙｚ平面の図</td>
+			<td>yz-plane</td>
 		</tr>
 		<tr>

@@ Line 207: / Line 207: @@
 ====Output file→3D<br>====
 	[[File:121p.3d-pdb2mrc2d.png]]<br>
-	<div>このOptionを使用した場合、二つ's imageに相違点はない</div>
+	<div>In this option, difference between 2 images is not.</div>
 <br>
-−
 === Option -Rot===
 ====-Rot 6 6に設定====

@@ Line 178: / Line 178: @@
 ===[[:Media:Input-121P-Move.pdb.zip|Input file]] image===
 	<div>[[File:121p-move-pdb2mrc2d.png]]<br>
-	pdbInfoでみたInput fileの詳細<br>
+	By [[pdbInfo]]<br>
 	[[File:121p-move-info-pdb2mrc2d.png]]<br></div>
 <br>
 ===Output file image===
-	<div>Optionを使用し、画像に物体が写るよう調整する<br>
+	<div>Use the options as the object falls within image.<br>
-	今回のInput fileでは下記のようにOptionを設定すると、物体がほぼ中心に写る<br></div>
+	In the case of this Input file, set the options as the following.<br></div>
 		<table border="1">

@@ Line 140: / Line 140: @@
 	*If you require axis at center, check by [[pdbInfo]], and execute [[pdbMove]] with Inverting + and -.</div>
-===RotModeの設定 details===
+===RotMode's details===
 	<table>
 		<tr>
-			<td>一桁目:</td>
+			<td>1st:</td>
-			<td>どの軸から回転を始めるか設定</td>
+			<td>1st rotation axis</td>
 		</tr>
 		<tr>
-			<td>二桁目:</td>
+			<td>2nd:</td>
-			<td>回転軸の順番を設定１</td>
+			<td>Setting1 of rotation order</td>
 		</tr>
 		<tr>
 			<td></td>
-			<td>O…Z→Y→Xの順に回転軸を変更する<br>
+			<td>O…Rotation Order: Z→Y→X<br>
-			E…Z→X→Yの順に回転軸を変更する</td>
+			E…Rotation Order: Z→X→Y</td>
 		</tr>
 		<tr>
-			<td>三桁目:</td>
+			<td>3rd:</td>
-			<td>回転軸の順番の設定２</td>
+			<td>Setting2 of rotation order</td>
 		</tr>
 		<tr>
 			<td></td>
-			<td>Y…順番を維持する<br>
+			<td>Y…keep the order<br>
-			N…順番を逆順にする</td>
+			N…reverse the order</td>
 		</tr>
 		<tr>
-			<td>四桁目:</td>
+			<td>4th:</td>
-			<td>回転方法を設定</td>
+			<td>Setting of rotation method</td>
 		</tr>
 		<tr>
 			<td></td>
-			<td>Y…物体そのものをまわす<br>
+			<td>Y…rotate object directly<br>
-			D…座標を移動させる</td>
+			D…rotate at coordinates</td>
 		</tr>
 	</table>
 == Execution example ==

@@ Line 119: / Line 119: @@
 		<tr>
 			<td>0</td>
-			<td>メルカトール図法・等角</td>
+			<td>Mercatol/equal angle</td>
 		</tr>
 		<tr>
 			<td>1</td>
-			<td>モルワイデ図法・等角</td>
+			<td>Morwide/equal angle</td>
 		</tr>
 		<tr>
 			<td>2</td>
-			<td>メルカトール図法・等積</td>
+			<td>Mercatol/equal area</td>
 		</tr>
 		<tr>
 			<td>3</td>
-			<td>モルワイデ図法・等積</td>
+			<td>Morwide/equal area</td>
 		</tr>
 		</div>
@@ Line 137: / Line 137: @@
 	<br>
 	<br>
-	<div>※Case: -Sと-startEAの両方が宣言されていた場合、-Sを実行した後に-startEAが実行される<br>
+	<div>If both of -s and -startEA, first -s and second -startEA will be performed.<br>
-	※軸を中心にもってきたい場合は、pdbInfoで軸を調べ、pdbMoveで軸の＋とーを逆にして実行する</div>
+	*If you require axis at center, check by [[pdbInfo]], and execute [[pdbMove]] with Inverting + and -.</div>
 ===RotModeの設定 details===

@@ Line 14: / Line 14: @@
 			<td>-i</td>
 			<td>Essential</td>
-			<td>Input設定: [[PDB]]</td>
+			<td>Input: [[PDB]]</td>
 			<td>NULL</td>
 		</tr>
@@ Line 20: / Line 20: @@
 			<td>-o</td>
 			<td>Optional</td>
-			<td>Output設定: [[mrcImage]](2D)</td>
+			<td>Output: [[mrcImage]](2D)</td>
 			<td>NULL</td>
 		</tr>
@@ Line 26: / Line 26: @@
 			<td>-O</td>
 			<td>Optional</td>
-			<td>Output設定: [[mrcImage]](3D)</td>
+			<td>Output: [[mrcImage]](3D)</td>
 			<td>NULL</td>
 		</tr>
@@ Line 32: / Line 32: @@
 			<td>-d</td>
 			<td>Essential</td>
-			<td>1ピクセルのWidthを指定</td>
+			<td>Width per 1pixel</td>
 			<td>5.0 5.0</td>
 		</tr>
@@ Line 38: / Line 38: @@
 			<td>-s</td>
 			<td>Optional</td>
-			<td>画像の位置を指定</td>
+			<td>Position of image</td>
 			<td>0.0 0.0</td>
 		</tr>
@@ Line 44: / Line 44: @@
 			<td>-n</td>
 			<td>Essential</td>
-			<td>画像のサイズを指定</td>
+			<td>Size of image</td>
 			<td>0 0</td>
 		</tr>
@@ Line 50: / Line 50: @@
 			<td>-Rot</td>
 			<td>Optional</td>
-			<td>回転（ｘ軸、ｙ軸のみ）</td>
+			<td>Rotaiton (x-axis, y-axis)</td>
 			<td>1 1</td>
 		</tr>
@@ Line 56: / Line 56: @@
 			<td>-S</td>
 			<td>Optional</td>
-			<td>Z軸→X軸→Y軸の順で回転</td>
+			<td>Rotation (order z-axis -> x-axis -> y-axis)</td>
 			<td>0.0 0.0 0.0</td>
 		</tr>
@@ Line 62: / Line 62: @@
 			<td>-startEA</td>
 			<td>Optional</td>
-			<td>[[Euler Angle]]を設定</td>
+			<td>[[Euler Angle]]</td>
 			<td>YOYS 0.0 0.0 0.0</td>
 		</tr>
@@ Line 68: / Line 68: @@
 			<td>-EAMode</td>
 			<td>Optional</td>
-			<td>RotationModeを指定</td>
+			<td>RotationMode</td>
 			<td>YOYS</td>
 		</tr>
@@ Line 74: / Line 74: @@
 			<td>-EARot1</td>
 			<td>Optional</td>
-			<td>主となる回転</td>
+			<td>FirstRotation</td>
 			<td>5.0 0.0 180.0</td>
 		</tr>
@@ Line 80: / Line 80: @@
 			<td>-EARot2</td>
 			<td>Optional</td>
-			<td>-EARot1とは別の回転</td>
+			<td>SecondRotation</td>
 			<td>5.0 0.0 180.0</td>
 		</tr>
@@ Line 86: / Line 86: @@
 			<td>-w</td>
 			<td>Optional</td>
-			<td>重量を設定</td>
+			<td>Weight</td>
 			<td>1.0</td>
 		</tr>
@@ Line 92: / Line 92: @@
 			<td>-sig</td>
 			<td>Optional</td>
-			<td>原子の半径を指定</td>
+			<td>Atom Radius: [A]</td>
 			<td>0.0</td>
 		</tr>
@@ Line 98: / Line 98: @@
 			<td>-m</td>
 			<td>Optional</td>
-			<td>Mode設定</td>
+			<td>Mode</td>
 			<td>0</td>
 		</tr>