Difference between revisions of "pdb2mrc2d"

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<td>-i</td>
 
<td>-i</td>
 
<td>Essential</td>
 
<td>Essential</td>
−
<td>Input設定: [[PDB]]</td>
+
<td>Input: [[PDB]]</td>
 
<td>NULL</td>
 
<td>NULL</td>
 
</tr>
 
</tr>
Line 20: Line 20:
 
<td>-o</td>
 
<td>-o</td>
 
<td>Optional</td>
 
<td>Optional</td>
−
<td>Output設定: [[mrcImage]](2D)</td>
+
<td>Output: [[mrcImage]](2D)</td>
 
<td>NULL</td>
 
<td>NULL</td>
 
</tr>
 
</tr>
Line 26: Line 26:
 
<td>-O</td>
 
<td>-O</td>
 
<td>Optional</td>
 
<td>Optional</td>
−
<td>Output設定: [[mrcImage]](3D)</td>
+
<td>Output: [[mrcImage]](3D)</td>
 
<td>NULL</td>
 
<td>NULL</td>
 
</tr>
 
</tr>
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<td>-d</td>
 
<td>-d</td>
 
<td>Essential</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>
 
<td>5.0 5.0</td>
 
</tr>
 
</tr>
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<td>-s</td>
 
<td>-s</td>
 
<td>Optional</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>
 
<td>0.0 0.0</td>
 
</tr>
 
</tr>
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<td>-n</td>
 
<td>-n</td>
 
<td>Essential</td>
 
<td>Essential</td>
−
<td>画像のサイズを指定</td>
+
<td>Size of image</td>
 
<td>0 0</td>
 
<td>0 0</td>
 
</tr>
 
</tr>
Line 50: Line 50:
 
<td>-Rot</td>
 
<td>-Rot</td>
 
<td>Optional</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>
 
<td>1 1</td>
 
</tr>
 
</tr>
Line 56: Line 56:
 
<td>-S</td>
 
<td>-S</td>
 
<td>Optional</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>
 
<td>0.0 0.0 0.0</td>
 
</tr>
 
</tr>
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<td>-startEA</td>
 
<td>-startEA</td>
 
<td>Optional</td>
 
<td>Optional</td>
−
<td>[[Euler Angle]]を設定</td>
+
<td>[[Euler Angle]]</td>
 
<td>YOYS 0.0 0.0 0.0</td>
 
<td>YOYS 0.0 0.0 0.0</td>
 
</tr>
 
</tr>
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<td>-EAMode</td>
 
<td>-EAMode</td>
 
<td>Optional</td>
 
<td>Optional</td>
−
<td>RotationModeを指定</td>
+
<td>RotationMode</td>
 
<td>YOYS</td>
 
<td>YOYS</td>
 
</tr>
 
</tr>
Line 74: Line 74:
 
<td>-EARot1</td>
 
<td>-EARot1</td>
 
<td>Optional</td>
 
<td>Optional</td>
−
<td>主となる回転</td>
+
<td>FirstRotation</td>
 
<td>5.0 0.0 180.0</td>
 
<td>5.0 0.0 180.0</td>
 
</tr>
 
</tr>
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<td>-EARot2</td>
 
<td>-EARot2</td>
 
<td>Optional</td>
 
<td>Optional</td>
−
<td>-EARot1とは別の回転</td>
+
<td>SecondRotation</td>
 
<td>5.0 0.0 180.0</td>
 
<td>5.0 0.0 180.0</td>
 
</tr>
 
</tr>
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<td>-w</td>
 
<td>-w</td>
 
<td>Optional</td>
 
<td>Optional</td>
−
<td>重量を設定</td>
+
<td>Weight</td>
 
<td>1.0</td>
 
<td>1.0</td>
 
</tr>
 
</tr>
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<td>-sig</td>
 
<td>-sig</td>
 
<td>Optional</td>
 
<td>Optional</td>
−
<td>原子の半径を指定</td>
+
<td>Atom Radius: [A]</td>
 
<td>0.0</td>
 
<td>0.0</td>
 
</tr>
 
</tr>
Line 98: Line 98:
 
<td>-m</td>
 
<td>-m</td>
 
<td>Optional</td>
 
<td>Optional</td>
−
<td>Mode設定</td>
+
<td>Mode</td>
 
<td>0</td>
 
<td>0</td>
 
</tr>
 
</tr>
Line 119: Line 119:
 
<tr>
 
<tr>
 
<td>0</td>
 
<td>0</td>
−
<td>メルカトール図法・等角</td>
+
<td>Mercatol/equal angle</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
 
<td>1</td>
 
<td>1</td>
−
<td>モルワイデ図法・等角</td>
+
<td>Morwide/equal angle</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
 
<td>2</td>
 
<td>2</td>
−
<td>メルカトール図法・等積</td>
+
<td>Mercatol/equal area</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
 
<td>3</td>
 
<td>3</td>
−
<td>モルワイデ図法・等積</td>
+
<td>Morwide/equal area</td>
 
</tr>
 
</tr>
 
</div>
 
</div>
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<br>
 
<br>
 
<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===
+
===RotMode's details===
 
<table>
 
<table>
 
<tr>
 
<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>
 
<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>
 
<tr>
 
<tr>
 
<td></td>
 
<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>
 
<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>
 
<tr>
 
<tr>
 
<td></td>
 
<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>
 
<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>
 
<tr>
 
<tr>
 
<td></td>
 
<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>
 
</tr>
 
</table>
 
</table>
−
 
  
 
== Execution example ==
 
== Execution example ==
 
===[[:Media:Input-121P-Move.pdb.zip|Input file]] image===
 
===[[:Media:Input-121P-Move.pdb.zip|Input file]] image===
 
<div>[[File:121p-move-pdb2mrc2d.png]]<br>
 
<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>
 
[[File:121p-move-info-pdb2mrc2d.png]]<br></div>
 
<br>
 
<br>
 
 
 
===Output file image===
 
===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">
 
<table border="1">
Line 208: Line 207:
 
====Output file→3D<br>====
 
====Output file→3D<br>====
 
[[File:121p.3d-pdb2mrc2d.png]]<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>
 
<br>
−
+
 
 
=== Option -Rot===
 
=== Option -Rot===
−
====-Rot 6 6に設定====
+
====Case: -Rot 6 6====
 
=====Output file→2D=====
 
=====Output file→2D=====
 
[[File:121p.2d-Rot-pdb2mrc2d.png]]
 
[[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>
 
<table>
 
<tr>
 
<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>
 
<tr>
 
<tr>
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=== Option -S===
 
=== Option -S===
−
====-Rot 6 6、-S 30 30 30に設定====
+
====Case: -Rot 6 6、-S 30 30 30====
 
=====Output file→2D=====
 
=====Output file→2D=====
 
[[File:121p.2d-S30-pdb2mrc2d.png]]
 
[[File:121p.2d-S30-pdb2mrc2d.png]]
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=== Option -startEA===
 
=== 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=====
 
=====Output file→2D=====
 
[[File:121p.2d-startEA30-pdb2mrc2d.png]]
 
[[File:121p.2d-startEA30-pdb2mrc2d.png]]
Line 242: Line 241:
 
 
 
=== Option -EAMode===
 
=== Option -EAMode===
−
====-Rot 6 6、-EAMode XOYSに設定====
+
====Case: -Rot 6 6、-EAMode XOYS====
 
=====Output file→2D=====
 
=====Output file→2D=====
 
[[File:121p.2d-EAMove-pdb2mrc2d.png]]
 
[[File:121p.2d-EAMove-pdb2mrc2d.png]]
 
<br>
 
<br>
  
−
====-Rot 6 6、-EAMode YOYSに設定====
+
====Case: -Rot 6 6、-EAMode YOYS====
 
=====Output file→2D=====
 
=====Output file→2D=====
 
[[File:121p.2d-EAModeY-pdb2mrc2d.png]]
 
[[File:121p.2d-EAModeY-pdb2mrc2d.png]]
Line 253: Line 252:
  
 
=== Option -EARot1,-EARot2===
 
=== 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=====
 
=====Output file→2D=====
 
[[File:121p.2d-EARot12-pdb2mrc2d.png]]
 
[[File:121p.2d-EARot12-pdb2mrc2d.png]]
Line 259: Line 258:
  
 
=== Option -sig===
 
=== 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]]
 
[[File:121p.2d-sig-pdb2mrc2d.png]]
 
<br>
 
<br>
  
 
=== Option -w===
 
=== 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]]
 
[[File:121p.2d-w1-pdb2mrc2d.png]]
 
<br>
 
<br>
  
−
====-w 10を指定した場合's imagedata====
+
====-w 10 image data====
 
[[File:121p.2d-w2-pdb2mrc2d.png]]
 
[[File:121p.2d-w2-pdb2mrc2d.png]]
 
<br>
 
<br>
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</table>
 
</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>

Latest revision as of 04:08, 7 August 2014

pdb2mrc2d Eos's Command that converts from PDB file to mrcImage file.

List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: PDB NULL
-o Optional Output: mrcImage(2D) NULL
-O Optional Output: mrcImage(3D) NULL
-d Essential Width per 1pixel 5.0 5.0
-s Optional Position of image 0.0 0.0
-n Essential Size of image 0 0
-Rot Optional Rotaiton (x-axis, y-axis) 1 1
-S Optional Rotation (order z-axis -> x-axis -> y-axis) 0.0 0.0 0.0
-startEA Optional Euler Angle YOYS 0.0 0.0 0.0
-EAMode Optional RotationMode YOYS
-EARot1 Optional FirstRotation 5.0 0.0 180.0
-EARot2 Optional SecondRotation 5.0 0.0 180.0
-w Optional Weight 1.0
-sig Optional Atom Radius: [A] 0.0
-m Optional Mode 0
-h Optional Help 　

-m details

Value Description
0 Mercatol/equal angle
1 Morwide/equal angle
2 Mercatol/equal area
3 Morwide/equal area



If both of -s and -startEA, first -s and second -startEA will be performed.
*If you require axis at center, check by pdbInfo, and execute pdbMove with Inverting + and -.

RotMode's details

1st: 1st rotation axis
2nd: Setting1 of rotation order
O…Rotation Order: Z→Y→X
E…Rotation Order: Z→X→Y
3rd: Setting2 of rotation order
Y…keep the order
N…reverse the order
4th: Setting of rotation method
Y…rotate object directly
D…rotate at coordinates

Execution example

Input file image

121p-move-pdb2mrc2d.png

By pdbInfo

121p-move-info-pdb2mrc2d.png


Output file image

Use the options as the object falls within image.
In the case of this Input file, set the options as the following.
-d 0.8 0.8
-s -40 -40
-n 100 100


Output file→2D

121p.2d-pdb2mrc2d.png

Output file→3D

121p.3d-pdb2mrc2d.png

In this option, difference between 2 images is not.


Option -Rot

Case: -Rot 6 6

Output file→2D

121p.2d-Rot-pdb2mrc2d.png

Output file→3D(Display at 3D by combining 2D result.)
xy-plane yz-plane
121p.3d-EAMode1-pdb2mrc2d.png 121p.3d-EAMode2-pdb2mrc2d.png


Option -S

Case: -Rot 6 6、-S 30 30 30

Output file→2D

121p.2d-S30-pdb2mrc2d.png

Option -startEA

Case: -Rot 6 6、-startEA XOYS 30 30 30

Output file→2D

121p.2d-startEA30-pdb2mrc2d.png

Option -EAMode

Case: -Rot 6 6、-EAMode XOYS

Output file→2D

121p.2d-EAMove-pdb2mrc2d.png

Case: -Rot 6 6、-EAMode YOYS

Output file→2D

121p.2d-EAModeY-pdb2mrc2d.png

Option -EARot1,-EARot2

Case: -EARot1 10 20 70,-EARot2 20 50 100

Output file→2D

121p.2d-EARot12-pdb2mrc2d.png

Option -sig

Case: -sig 1, Output file is -o

121p.2d-sig-pdb2mrc2d.png

Option -w

Case: -w 10, Output file is -o

without -w image data

121p.2d-w1-pdb2mrc2d.png

-w 10 image data

121p.2d-w2-pdb2mrc2d.png

Option -m

Case: m=0
121p.2d-pdb2mrc2d.png m0-pdb2mrc2d.png
Case: m=1
121p.2d-m1-pdb2mrc2d.png File:m1-pdb2mrc2d.png
Case: m=2
121p.2d-m2-pdb2mrc2d.png File:m2-pdb2mrc2d.png
Case: m=3
121p.2d-m3-pdb2mrc2d.png File:m3-pdb2mrc2d.png
In this time, It is not easy to see these difference. But, you can see it by image data details.
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