Difference between revisions of "pdb2mrc2d"
From EosPedia
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(→RotModeの設定 details) |
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*If you require axis at center, check by [[pdbInfo]], and execute [[pdbMove]] with Inverting + and -.</div> | *If you require axis at center, check by [[pdbInfo]], and execute [[pdbMove]] with Inverting + and -.</div> | ||
| − | === | + | ===RotMode's details=== |
<table> | <table> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>1st:</td> |
| − | <td> | + | <td>1st rotation axis</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>2nd:</td> |
| − | <td> | + | <td>Setting1 of rotation order</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td></td> | <td></td> | ||
| − | <td> | + | <td>O…Rotation Order: Z→Y→X<br> |
| − | + | E…Rotation Order: Z→X→Y</td> | |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>3rd:</td> |
| − | <td> | + | <td>Setting2 of rotation order</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td></td> | <td></td> | ||
| − | <td> | + | <td>Y…keep the order<br> |
| − | + | N…reverse the order</td> | |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td> | + | <td>4th:</td> |
| − | <td> | + | <td>Setting of rotation method</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td></td> | <td></td> | ||
| − | <td> | + | <td>Y…rotate object directly<br> |
| − | + | D…rotate at coordinates</td> | |
</tr> | </tr> | ||
</table> | </table> | ||
| − | |||
== Execution example == | == Execution example == | ||
Revision as of 03:08, 7 August 2014
pdb2mrc2d Eos's Command that converts from PDB file to mrcImage file.
Contents
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 -.
*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
pdbInfoでみたInput fileの詳細
Output file image
Optionを使用し、画像に物体が写るよう調整する
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
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
| -d | 0.8 0.8 |
| -s | -40 -40 |
| -n | 100 100 |
Output file→2D
Output file→3D
このOptionを使用した場合、二つ's imageに相違点はない
Option -Rot
-Rot 6 6に設定
Output file→2D
Output file→3D（2Dの結果を繋ぎ、3Dで出力している）
| ｘｙ平面の図 | ｙｚ平面の図 |
 |
 |
Option -S
-Rot 6 6、-S 30 30 30に設定
Output file→2D
Option -startEA
-Rot 6 6、-startEA XOYS 30 30 30に設定
Output file→2D
Option -EAMode
-Rot 6 6、-EAMode XOYSに設定
Output file→2D
-Rot 6 6、-EAMode YOYSに設定
Output file→2D
Option -EARot1,-EARot2
-EARot1 10 20 70,-EARot2 20 50 100に設定
Output file→2D
Option -sig
-sig 1に設定、Output fileは-oとする
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
-w 10を指定した場合's imagedata
Option -m
| Case: m=0 | |
|
 |
| Case: m=1 | |
 |
File:m1-pdb2mrc2d.png |
| Case: m=2 | |
 |
File:m2-pdb2mrc2d.png |
| Case: m=3 | |
 |
File:m3-pdb2mrc2d.png |
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
