「pdb2SketchMacro」の版間の差分
提供: Eospedia
| 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> | ||
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
