「pdb2SketchMacro」の版間の差分

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移動: 案内検索
(Kinoshita がページ「Pdb2SketchMacro」を「pdb2SketchMacro」に移動しました)
行47: 行47:
 
<td> </td>  
 
<td> </td>  
 
</tr>  
 
</tr>  
</table>  
+
</table>
 +
<br>  
  
 
===モードの詳細===
 
===モードの詳細===
行72: 行73:
 
</tr>  
 
</tr>  
 
</table>  
 
</table>  
 
+
<br>
  
 
== 実行例 ==
 
== 実行例 ==
===入力ファイルの画像===
+
===[[:Media:Input-121P.pdb.zip|入力ファイル]]の画像===
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
<td>[[画像:Input-pdb2SketchMacro.png]]</td>  
+
<td>[[画像:Input-121P-PDB.png]]</td>  
 
<td><p align="left">重心<br>  
 
<td><p align="left">重心<br>  
 
最大半径<br>  
 
最大半径<br>  
 
最大半径(座標)<br> </p>
 
最大半径(座標)<br> </p>
 
</td>  
 
</td>  
<td><p align="left">-4.617250e-01  -2.186292e-01   -5.402542e+00<br>  
+
<td><p align="left">6.053012e+00    2.519590e+01    1.189075e+01<br>  
3.823869e+01 <br>  
+
3.286664e+01 <br>  
35.07     22.99     20.84 <br></p>
+
24.77     23.85     28.04<br></p>
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
</table>
+
</table>
 +
<br>
  
 
===オプション必須項目のみの場合===
 
===オプション必須項目のみの場合===
 
<pre>
 
<pre>
sam_atom_in /Input.pdb  TS
+
sam_atom_in Input.pdb  TS
sketch_object TSH__1
+
sketch_object TSH_A1
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_type  Spiral
 
sketch_type  Spiral
paint_zone TS A10 A14 red
+
paint_zone TS A16 A25 red
sketch_add    TS A10 A14
+
sketch_add    TS A16 A25
 
end_object
 
end_object
sketch_object TSH__2
+
sketch_object TSH_A2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_type  Spiral
 
sketch_type  Spiral
paint_zone TS A18 A35 red
+
paint_zone TS A65 A74 red
sketch_add    TS A18 A35
+
sketch_add    TS A65 A74
 
end_object
 
end_object
sketch_object TSH__3
+
sketch_object TSH_A3
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_type  Spiral
 
sketch_type  Spiral
paint_zone TS A51  A63 red
+
paint_zone TS A87 A103 red
sketch_add    TS A51 A63
+
sketch_add    TS A87 A103
 
end_object
 
end_object
sketch_object TSH__4
+
sketch_object TSH_A4
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_type  Spiral
 
sketch_type  Spiral
paint_zone TS A66  A70  red
+
paint_zone TS A127 A137 red
sketch_add    TS A66  A70
+
sketch_add    TS A127 A137
 
end_object
 
end_object
sketch_object TSH__5
+
sketch_object TSH_A5
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_type  Spiral
 
sketch_type  Spiral
paint_zone TS A72  A81  red
+
paint_zone TS A152 A164 red
sketch_add    TS A72  A81
+
sketch_add    TS A152 A164
end_object
+
sketch_object TSH__6
+
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
+
sketch_type  Spiral
+
paint_zone TS A87  A101 red
+
sketch_add    TS A87  A101
+
 
end_object
 
end_object
 +
sketch_object TSS__S
 +
sketch_setup  Arrow solid 2.5 0.5 3.75 2 7 3 2
 +
sketch_type  Arrow
 +
paint_zone TS A37  A46  blue
 +
sketch_add    TS A37  A46
 +
paint_zone TS A49  A58  blue
 +
sketch_add    TS A49  A58
 +
paint_zone TS A2  A9  blue
 +
sketch_add    TS A2  A9 
 +
paint_zone TS A77  A83  blue
 +
sketch_add    TS A77  A83
 +
paint_zone TS A111 A116 blue
 +
sketch_add    TS A111 A116
 +
paint_zone TS A141 A143 blue
 +
sketch_add    TS A141 A143
 +
end_oject
 
sketch_object TSN__1
 
sketch_object TSN__1
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_type  Rattler  
 
sketch_type  Rattler  
paint_zone TS A1  A10  white
+
paint_zone TS A1  A2  white
sketch_add    TS A1  A10
+
sketch_add    TS A1  A2 
 
end_object
 
end_object
 
sketch_object TSN__2
 
sketch_object TSN__2
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_type  Rattler  
 
sketch_type  Rattler  
paint_zone TS A14  A18 white
+
paint_zone TS A9  A16 white
sketch_add    TS A14  A18
+
sketch_add    TS A9   A16
end_object
+
sketch_object TSN__3
+
sketch_setup  Rattler solid 0.5 7 2
+
sketch_type   Rattler
+
paint_zone TS A35  A51  white
+
sketch_add    TS A35  A51
+
 
end_object
 
end_object
  
 
-中略-
 
-中略-
  
sketch_object TSN_48
+
sketch_object TSN_11
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_type  Rattler  
 
sketch_type  Rattler  
paint_zone TS A81  A87  white
+
paint_zone TS A143 A152 white
sketch_add    TS A81  A87
+
sketch_add    TS A143 A152
 
end_object
 
end_object
sketch_object TSN_49
+
sketch_object TSN_12
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_type  Rattler  
 
sketch_type  Rattler  
paint_zone TS A101 0  white
+
paint_zone TS A164 0  white
sketch_add    TS A101 0   
+
sketch_add    TS A164 0   
 
end_object
 
end_object
 
</pre>
 
</pre>
 +
<br>
  
 
===オプション -m===
 
===オプション -m===
 
====m=1で実行====  
 
====m=1で実行====  
 
<pre>
 
<pre>
sam_atom_in /Input.pdb  TS
+
sam_atom_in Input.pdb  TS
sketch_object TSH__1
+
sketch_object TSH_A1
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_type  Spiral
 
sketch_type  Spiral
paint_zone TS A10 A14 red
+
paint_zone TS A16 A25 red
sketch_add    TS A10 A14
+
sketch_add    TS A16 A25
 
end_object
 
end_object
sketch_object TSH__2
+
sketch_object TSH_A2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_type  Spiral
 
sketch_type  Spiral
paint_zone TS A18 A35 red
+
paint_zone TS A65 A74 red
sketch_add    TS A18 A35
+
sketch_add    TS A65 A74
 
end_object
 
end_object
sketch_object TSH__3
+
sketch_object TSH_A3
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_type  Spiral
 
sketch_type  Spiral
paint_zone TS A51  A63 red
+
paint_zone TS A87 A103 red
sketch_add    TS A51 A63
+
sketch_add    TS A87 A103
 
end_object
 
end_object
sketch_object TSH__4
+
sketch_object TSH_A4
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_type  Spiral
 
sketch_type  Spiral
paint_zone TS A66  A70  red
+
paint_zone TS A127 A137 red
sketch_add    TS A66  A70
+
sketch_add    TS A127 A137
 
end_object
 
end_object
sketch_object TSH__5
+
sketch_object TSH_A5
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
 
sketch_type  Spiral
 
sketch_type  Spiral
paint_zone TS A72  A81  red
+
paint_zone TS A152 A164 red
sketch_add    TS A72  A81
+
sketch_add    TS A152 A164
end_object
+
sketch_object TSH__6
+
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
+
sketch_type  Spiral
+
paint_zone TS A87  A101 red
+
sketch_add    TS A87  A101
+
 
end_object
 
end_object
 
</pre>
 
</pre>
 +
<br>
  
 
====m=8で実行====  
 
====m=8で実行====  
 
<pre>
 
<pre>
sam_atom_in /Input.pdb  TS
+
sam_atom_in Input.pdb  TS
 
sketch_object TSN__1
 
sketch_object TSN__1
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_type  Rattler  
 
sketch_type  Rattler  
paint_zone TS A1  A10  white
+
paint_zone TS A1  A2  white
sketch_add    TS A1  A10
+
sketch_add    TS A1  A2 
 
end_object
 
end_object
 
sketch_object TSN__2
 
sketch_object TSN__2
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_type  Rattler  
 
sketch_type  Rattler  
paint_zone TS A14  A18 white
+
paint_zone TS A9  A16 white
sketch_add    TS A14  A18
+
sketch_add    TS A9   A16
end_object
+
sketch_object TSN__3
+
sketch_setup  Rattler solid 0.5 7 2
+
sketch_type   Rattler
+
paint_zone TS A35  A51  white
+
sketch_add    TS A35  A51
+
 
end_object
 
end_object
  
 
-中略-
 
-中略-
  
sketch_object TSN_48
+
sketch_object TSN_11
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_type  Rattler  
 
sketch_type  Rattler  
paint_zone TS A81  A87  white
+
paint_zone TS A143 A152 white
sketch_add    TS A81  A87
+
sketch_add    TS A143 A152
 
end_object
 
end_object
sketch_object TSN_49
+
sketch_object TSN_12
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_setup  Rattler solid 0.5 7 2
 
sketch_type  Rattler  
 
sketch_type  Rattler  
paint_zone TS A101 0  white
+
paint_zone TS A164 0  white
sketch_add    TS A101 0   
+
sketch_add    TS A164 0   
 
end_object
 
end_object
 
</pre>
 
</pre>

2014年2月13日 (木) 07:57時点における版

pdb2SketchMacroとはEosコマンドである。


オプション一覧

メインオプション

オプション 必須項目/選択項目 説明 デフォルト
-i 選択 入力ファイル: [pdb] stdin
-o 選択 出力ファイル: [テキスト] stdout
-MolName 選択 分子名(2文字以下が望ましい) TS
-c 選択 コンフィグファイル設定 NULL
-m 選択 モードを設定 15
-h 選択 ヘルプを表示  


モードの詳細

モード 説明
1 Helix sketched with spirals
2 Sheet sketched with arrows
4 Turn sketched with rattler
8 No structure sketched with rattler


実行例

入力ファイルの画像

Input-121P-PDB.png

重心

最大半径

最大半径(座標)

6.053012e+00 2.519590e+01 1.189075e+01

3.286664e+01

24.77 23.85 28.04


オプション必須項目のみの場合

sam_atom_in Input.pdb  TS
sketch_object TSH_A1
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A16  A25  red
sketch_add    TS A16  A25 
end_object
sketch_object TSH_A2
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A65  A74  red
sketch_add    TS A65  A74 
end_object
sketch_object TSH_A3
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A87  A103 red
sketch_add    TS A87  A103
end_object
sketch_object TSH_A4
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A127 A137 red
sketch_add    TS A127 A137
end_object
sketch_object TSH_A5
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A152 A164 red
sketch_add    TS A152 A164
end_object
sketch_object TSS__S
sketch_setup  Arrow solid 2.5 0.5 3.75 2 7 3 2
sketch_type   Arrow 
paint_zone TS A37  A46  blue
sketch_add    TS A37  A46 
paint_zone TS A49  A58  blue
sketch_add    TS A49  A58 
paint_zone TS A2   A9   blue
sketch_add    TS A2   A9  
paint_zone TS A77  A83  blue
sketch_add    TS A77  A83 
paint_zone TS A111 A116 blue
sketch_add    TS A111 A116
paint_zone TS A141 A143 blue
sketch_add    TS A141 A143
end_oject
sketch_object TSN__1
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A1   A2   white
sketch_add    TS A1   A2  
end_object
sketch_object TSN__2
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A9   A16  white
sketch_add    TS A9   A16 
end_object

-中略-

sketch_object TSN_11
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A143 A152 white
sketch_add    TS A143 A152
end_object
sketch_object TSN_12
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A164 0   white
sketch_add    TS A164 0  
end_object


オプション -m

m=1で実行

sam_atom_in Input.pdb  TS
sketch_object TSH_A1
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A16  A25  red
sketch_add    TS A16  A25 
end_object
sketch_object TSH_A2
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A65  A74  red
sketch_add    TS A65  A74 
end_object
sketch_object TSH_A3
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A87  A103 red
sketch_add    TS A87  A103
end_object
sketch_object TSH_A4
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A127 A137 red
sketch_add    TS A127 A137
end_object
sketch_object TSH_A5
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A152 A164 red
sketch_add    TS A152 A164
end_object


m=8で実行

sam_atom_in Input.pdb  TS
sketch_object TSN__1
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A1   A2   white
sketch_add    TS A1   A2  
end_object
sketch_object TSN__2
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A9   A16  white
sketch_add    TS A9   A16 
end_object

-中略-

sketch_object TSN_11
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A143 A152 white
sketch_add    TS A143 A152
end_object
sketch_object TSN_12
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A164 0   white
sketch_add    TS A164 0  
end_object