「pdb2SketchMacro」の版間の差分
提供: Eospedia
細 (Kinoshita がページ「Pdb2SketchMacro」を「pdb2SketchMacro」に移動しました) |
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(同じ利用者による、間の2版が非表示) | |||
行14: | 行14: | ||
<td>-i</td> | <td>-i</td> | ||
<td>選択</td> | <td>選択</td> | ||
− | <td>入力ファイル: [ | + | <td>入力ファイル: [[PDB]]</td> |
<td>stdin</td> | <td>stdin</td> | ||
</tr> | </tr> | ||
行20: | 行20: | ||
<td>-o</td> | <td>-o</td> | ||
<td>選択</td> | <td>選択</td> | ||
− | <td>出力ファイル: [ | + | <td>出力ファイル: [[ASCII]]</td> |
<td>stdout</td> | <td>stdout</td> | ||
</tr> | </tr> | ||
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 == | ||
− | === | + | ===[[:Media:Input-121P.pdb.zip|入力ファイル]]の画像=== |
<table> | <table> | ||
<tr> | <tr> | ||
− | <td>[[画像:Input- | + | <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"> | + | <td><p align="left">6.053012e+00 2.519590e+01 1.189075e+01<br> |
− | 3. | + | 3.286664e+01 <br> |
− | + | 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 | + | sam_atom_in Input.pdb TS |
− | sketch_object | + | 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 | + | paint_zone TS A16 A25 red |
− | sketch_add TS | + | sketch_add TS A16 A25 |
end_object | end_object | ||
− | sketch_object | + | 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 | + | paint_zone TS A65 A74 red |
− | sketch_add TS | + | sketch_add TS A65 A74 |
end_object | end_object | ||
− | sketch_object | + | 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 | + | paint_zone TS A87 A103 red |
− | sketch_add TS | + | sketch_add TS A87 A103 |
end_object | end_object | ||
− | sketch_object | + | 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 | + | paint_zone TS A127 A137 red |
− | sketch_add TS | + | sketch_add TS A127 A137 |
end_object | end_object | ||
− | sketch_object | + | 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 | + | paint_zone TS A152 A164 red |
− | sketch_add TS | + | sketch_add TS A152 A164 |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
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 | + | paint_zone TS A1 A2 white |
− | sketch_add TS A1 | + | 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 | + | paint_zone TS A9 A16 white |
− | sketch_add TS | + | sketch_add TS A9 A16 |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
end_object | end_object | ||
-中略- | -中略- | ||
− | sketch_object | + | 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 | + | paint_zone TS A143 A152 white |
− | sketch_add TS | + | sketch_add TS A143 A152 |
end_object | end_object | ||
− | sketch_object | + | 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 | + | paint_zone TS A164 0 white |
− | sketch_add TS | + | 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 | + | sam_atom_in Input.pdb TS |
− | sketch_object | + | 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 | + | paint_zone TS A16 A25 red |
− | sketch_add TS | + | sketch_add TS A16 A25 |
end_object | end_object | ||
− | sketch_object | + | 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 | + | paint_zone TS A65 A74 red |
− | sketch_add TS | + | sketch_add TS A65 A74 |
end_object | end_object | ||
− | sketch_object | + | 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 | + | paint_zone TS A87 A103 red |
− | sketch_add TS | + | sketch_add TS A87 A103 |
end_object | end_object | ||
− | sketch_object | + | 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 | + | paint_zone TS A127 A137 red |
− | sketch_add TS | + | sketch_add TS A127 A137 |
end_object | end_object | ||
− | sketch_object | + | 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 | + | paint_zone TS A152 A164 red |
− | sketch_add TS | + | sketch_add TS A152 A164 |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
end_object | end_object | ||
</pre> | </pre> | ||
+ | <br> | ||
====m=8で実行==== | ====m=8で実行==== | ||
<pre> | <pre> | ||
− | sam_atom_in | + | 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 | + | paint_zone TS A1 A2 white |
− | sketch_add TS A1 | + | 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 | + | paint_zone TS A9 A16 white |
− | sketch_add TS | + | sketch_add TS A9 A16 |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
end_object | end_object | ||
-中略- | -中略- | ||
− | sketch_object | + | 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 | + | paint_zone TS A143 A152 white |
− | sketch_add TS | + | sketch_add TS A143 A152 |
end_object | end_object | ||
− | sketch_object | + | 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 | + | paint_zone TS A164 0 white |
− | sketch_add TS | + | sketch_add TS A164 0 |
+ | end_object | ||
+ | </pre> | ||
+ | <br> | ||
+ | |||
+ | ===オプション -MolName=== | ||
+ | ====MolName=XX, m=1で実行==== | ||
+ | <pre> | ||
+ | Input.pdb XX | ||
+ | sketch_object XXH_A1 | ||
+ | sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 | ||
+ | sketch_type Spiral | ||
+ | paint_zone XX A16 A25 red | ||
+ | sketch_add XX A16 A25 | ||
+ | end_object | ||
+ | sketch_object XXH_A2 | ||
+ | sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 | ||
+ | sketch_type Spiral | ||
+ | paint_zone XX A65 A74 red | ||
+ | sketch_add XX A65 A74 | ||
+ | end_object | ||
+ | sketch_object XXH_A3 | ||
+ | sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 | ||
+ | sketch_type Spiral | ||
+ | paint_zone XX A87 A103 red | ||
+ | sketch_add XX A87 A103 | ||
+ | end_object | ||
+ | sketch_object XXH_A4 | ||
+ | sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 | ||
+ | sketch_type Spiral | ||
+ | paint_zone XX A127 A137 red | ||
+ | sketch_add XX A127 A137 | ||
+ | end_object | ||
+ | sketch_object XXH_A5 | ||
+ | sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 | ||
+ | sketch_type Spiral | ||
+ | paint_zone XX A152 A164 red | ||
+ | sketch_add XX A152 A164 | ||
end_object | end_object | ||
</pre> | </pre> | ||
+ | <br> |
2014年8月7日 (木) 05:40時点における最新版
目次
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: ASCII | 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
重心 最大半径 |
6.053012e+00 2.519590e+01 1.189075e+01 3.286664e+01 |
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
オプション -MolName
MolName=XX, m=1で実行
Input.pdb XX sketch_object XXH_A1 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone XX A16 A25 red sketch_add XX A16 A25 end_object sketch_object XXH_A2 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone XX A65 A74 red sketch_add XX A65 A74 end_object sketch_object XXH_A3 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone XX A87 A103 red sketch_add XX A87 A103 end_object sketch_object XXH_A4 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone XX A127 A137 red sketch_add XX A127 A137 end_object sketch_object XXH_A5 sketch_setup Spiral solid 2.5 0.5 0.5 2 7 3 2 sketch_type Spiral paint_zone XX A152 A164 red sketch_add XX A152 A164 end_object