pdbSurface
提供: Eospedia
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-
