Difference between revisions of "pdb2mrc2d"
From EosPedia
(→RotModeの設定 details) |
(→Execution example) |
||
| Line 178: | Line 178: | ||
===[[: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> | ||
| − | + | 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> | + | <div>Use the options as the object falls within image.<br> |
| − | + | In the case of this Input file, set the options as the following.<br></div> | |
<table border="1"> | <table border="1"> | ||
Revision as of 03:09, 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
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.
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
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
