「pdbSurface」の版間の差分
提供: Eospedia
細 (Kinoshita がページ「PdbSurface」を「pdbSurface」に移動しました) |
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行1: | 行1: | ||
− | '''pdbSurface'''とは[[Eos]]の[[コマンド]]である。 | + | '''pdbSurface'''とは[[PDB]]から表面上の原子情報を得る[[Eos]]の[[コマンド]]である。 |
行14: | 行14: | ||
<td>-i</td> | <td>-i</td> | ||
<td>必須</td> | <td>必須</td> | ||
− | <td>入力ファイル: [ | + | <td>入力ファイル: [[PDB]]</td> |
<td>NULL</td> | <td>NULL</td> | ||
</tr> | </tr> | ||
行20: | 行20: | ||
<td>-o</td> | <td>-o</td> | ||
<td>必須</td> | <td>必須</td> | ||
− | <td>出力ファイル: [ | + | <td>出力ファイル: [[PDB]]</td> |
<td>NULL</td> | <td>NULL</td> | ||
</tr> | </tr> | ||
行26: | 行26: | ||
<td>-order</td> | <td>-order</td> | ||
<td>選択</td> | <td>選択</td> | ||
− | <td>order [A]</td> | + | <td>order: [A]</td> |
<td>1.7</td> | <td>1.7</td> | ||
</tr> | </tr> | ||
行78: | 行78: | ||
</tr> | </tr> | ||
</table> | </table> | ||
+ | <br> | ||
===モードの詳細=== | ===モードの詳細=== | ||
行90: | 行91: | ||
</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> | ||
+ | <tr> | ||
+ | <td>[[画像:Input-121P-PDB.png]]</td> | ||
+ | <td><p align="left">重心<br> | ||
+ | 最大半径<br> | ||
+ | 最大半径(座標)<br> </p> | ||
+ | </td> | ||
+ | <td><p align="left">6.053012e+00 2.519590e+01 1.189075e+01<br> | ||
+ | 3.286664e+01 <br> | ||
+ | 24.77 23.85 28.04<br></p> | ||
+ | </td> | ||
+ | </tr> | ||
+ | </table> | ||
+ | <br> | ||
+ | <div>入力データ(一部)</div> | ||
+ | <pre> | ||
+ | -前略- | ||
+ | |||
+ | ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00 14.06 N | ||
+ | ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 17.27 C | ||
+ | ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 16.41 C | ||
+ | ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 16.12 O | ||
+ | ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 17.94 C | ||
+ | ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 19.41 C | ||
+ | ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 21.82 S | ||
+ | ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00 23.68 C | ||
+ | ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 15.08 N | ||
+ | ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 16.71 C | ||
+ | |||
+ | -後略- | ||
+ | </pre> | ||
+ | <br> | ||
+ | |||
+ | ===オプション必須項目のみの場合=== | ||
+ | <div>出力データ(一部)</div> | ||
+ | <pre> | ||
+ | -前略- | ||
+ | |||
+ | ↓温度因子の項目が変化している | ||
+ | |||
+ | ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N | ||
+ | ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 72.48 0 C | ||
+ | ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 3.60 0 C | ||
+ | ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 52.08 0 O | ||
+ | ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C | ||
+ | ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C | ||
+ | ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 21.50 0 S | ||
+ | ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C | ||
+ | ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.93 0 N | ||
+ | ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 3.23 0 C | ||
+ | |||
+ | -後略- | ||
+ | </pre> | ||
+ | <br> | ||
+ | |||
+ | ===オプション -order=== | ||
+ | ====order=1.9で実行==== | ||
+ | <pre> | ||
+ | -前略- | ||
+ | |||
+ | ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N | ||
+ | ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 24.74 0 C | ||
+ | ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.05 0 C | ||
+ | ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 8.75 0 O | ||
+ | ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 34.92 0 C | ||
+ | ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 0.12 0 C | ||
+ | ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 5.53 0 S | ||
+ | ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C | ||
+ | ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.12 0 N | ||
+ | ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.00 0 C | ||
+ | |||
+ | -後略- | ||
+ | </pre> | ||
+ | <br> | ||
+ | |||
+ | ===オプション -refine=== | ||
+ | ====refine=1で実行==== | ||
+ | <pre> | ||
+ | -前略- | ||
+ | |||
+ | ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N | ||
+ | ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 17.24 0 C | ||
+ | ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 16.69 0 C | ||
+ | ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00100.00 0 O | ||
+ | ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 32.91 0 C | ||
+ | ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 9.69 0 C | ||
+ | ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 68.76 0 S | ||
+ | ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00 68.76 0 C | ||
+ | ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 16.69 0 N | ||
+ | ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 26.46 0 C | ||
+ | |||
+ | -後略- | ||
+ | </pre> | ||
+ | <br> | ||
+ | |||
+ | ===オプション -size=== | ||
+ | ====size=5で実行==== | ||
+ | <pre> | ||
+ | -前略- | ||
+ | |||
+ | ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N | ||
+ | ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00100.00 0 C | ||
+ | ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 32.30 0 C | ||
+ | ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 90.33 0 O | ||
+ | ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C | ||
+ | ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C | ||
+ | ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 42.23 0 S | ||
+ | ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C | ||
+ | ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 8.91 0 N | ||
+ | ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 12.07 0 C | ||
+ | |||
+ | -後略- | ||
+ | </pre> | ||
+ | <br> | ||
+ | |||
+ | ===オプション -mergin=2.8=== | ||
+ | ====mergin=2.8で実行==== | ||
+ | <pre> | ||
+ | -前略- | ||
+ | |||
+ | ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N | ||
+ | ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00100.00 0 C | ||
+ | ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 3.60 0 C | ||
+ | ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 52.08 0 O | ||
+ | ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C | ||
+ | ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C | ||
+ | ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 96.55 0 S | ||
+ | ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C | ||
+ | ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 12.72 0 N | ||
+ | ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C | ||
+ | |||
+ | -後略- | ||
+ | </pre> | ||
+ | <br> | ||
+ | |||
+ | ===オプション -thres=== | ||
+ | ====thres=0.1で実行==== | ||
+ | <pre> | ||
+ | -前略- | ||
+ | |||
+ | ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N | ||
+ | ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 37.57 0 C | ||
+ | ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.46 0 C | ||
+ | ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 32.12 0 O | ||
+ | ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 62.40 0 C | ||
+ | ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 36.08 0 C | ||
+ | ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 12.52 0 S | ||
+ | ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C | ||
+ | ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.53 0 N | ||
+ | ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C | ||
+ | |||
+ | -後略- | ||
+ | </pre> | ||
+ | <br> | ||
+ | |||
+ | ===オプション -weight=== | ||
+ | ====weight=1000, thres=0.1で実行==== | ||
+ | <pre> | ||
+ | -前略- | ||
+ | |||
+ | ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N | ||
+ | ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 37.57 0 C | ||
+ | ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.46 0 C | ||
+ | ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 32.12 0 O | ||
+ | ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 62.40 0 C | ||
+ | ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 36.08 0 C | ||
+ | ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 12.52 0 S | ||
+ | ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C | ||
+ | ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.53 0 N | ||
+ | ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C | ||
+ | |||
+ | -後略- | ||
+ | </pre> | ||
+ | <br> |
2014年2月14日 (金) 07:03時点における最新版
pdbSurfaceとはPDBから表面上の原子情報を得るEosのコマンドである。
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 | 必須 | 入力ファイル: PDB | NULL |
-o | 必須 | 出力ファイル: PDB | NULL |
-order | 選択 | order: [A] | 1.7 |
-refine | 選択 | Refine: Meshsize = Order/Refine | 2 |
-size | 選択 | Refine: Shell thickness = Order/Refine*Size | 3 |
-weight | 選択 | weight | 100.0 |
-mergin | 選択 | SearchArea | 3.0 |
-thres | 選択 | 閾値 | 0.0 |
-c | 選択 | コンフィグファイル設定 | NULL |
-m | 選択 | モードを設定 | 0 |
-h | 選択 | ヘルプを表示 |
モードの詳細
モード | 説明 |
---|---|
0 |
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 |
入力データ(一部)
-前略- ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00 14.06 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 17.27 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 16.41 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 16.12 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 17.94 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 19.41 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 21.82 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00 23.68 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 15.08 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 16.71 C -後略-
オプション必須項目のみの場合
出力データ(一部)
-前略- ↓温度因子の項目が変化している ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 72.48 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 3.60 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 52.08 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 21.50 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.93 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 3.23 0 C -後略-
オプション -order
order=1.9で実行
-前略- ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 24.74 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.05 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 8.75 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 34.92 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 0.12 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 5.53 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.12 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.00 0 C -後略-
オプション -refine
refine=1で実行
-前略- ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 17.24 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 16.69 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00100.00 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 32.91 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 9.69 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 68.76 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00 68.76 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 16.69 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 26.46 0 C -後略-
オプション -size
size=5で実行
-前略- ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00100.00 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 32.30 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 90.33 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 42.23 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 8.91 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 12.07 0 C -後略-
オプション -mergin=2.8
mergin=2.8で実行
-前略- ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00100.00 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 3.60 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 52.08 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00100.00 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00100.00 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 96.55 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 12.72 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C -後略-
オプション -thres
thres=0.1で実行
-前略- ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 37.57 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.46 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 32.12 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 62.40 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 36.08 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 12.52 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.53 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C -後略-
オプション -weight
weight=1000, thres=0.1で実行
-前略- ATOM 1 N MET A 1 -7.176 32.630 -6.655 1.00100.00 0 N ATOM 2 CA MET A 1 -5.913 31.928 -6.676 1.00 37.57 0 C ATOM 3 C MET A 1 -5.903 30.860 -5.600 1.00 1.46 0 C ATOM 4 O MET A 1 -6.703 30.881 -4.654 1.00 32.12 0 O ATOM 5 CB MET A 1 -4.712 32.869 -6.415 1.00 62.40 0 C ATOM 6 CG MET A 1 -4.594 33.420 -4.990 1.00 36.08 0 C ATOM 7 SD MET A 1 -3.193 34.558 -4.899 1.00 12.52 0 S ATOM 8 CE MET A 1 -4.325 35.886 -4.618 1.00100.00 0 C ATOM 9 N THR A 2 -4.966 29.934 -5.760 1.00 0.53 0 N ATOM 10 CA THR A 2 -4.759 28.930 -4.751 1.00 0.93 0 C -後略-