pdb2SketchMacro

提供: Eospedia
2013年12月10日 (火) 02:41時点におけるKinoshita (トーク | 投稿記録)による版

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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-pdb2SketchMacro.png

重心

最大半径

最大半径(座標)

-4.617250e-01 -2.186292e-01 -5.402542e+00

3.823869e+01

35.07 22.99 20.84

オプション必須項目のみの場合

sam_atom_in /Input.pdb  TS
sketch_object TSH__1
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A10  A14  red
sketch_add    TS A10  A14 
end_object
sketch_object TSH__2
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A18  A35  red
sketch_add    TS A18  A35 
end_object
sketch_object TSH__3
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A51  A63  red
sketch_add    TS A51  A63 
end_object
sketch_object TSH__4
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A66  A70  red
sketch_add    TS A66  A70 
end_object
sketch_object TSH__5
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A72  A81  red
sketch_add    TS A72  A81 
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
sketch_object TSN__1
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A1   A10  white
sketch_add    TS A1   A10 
end_object
sketch_object TSN__2
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A14  A18  white
sketch_add    TS A14  A18 
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

-中略-

sketch_object TSN_48
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A81  A87  white
sketch_add    TS A81  A87 
end_object
sketch_object TSN_49
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A101 0   white
sketch_add    TS A101 0  
end_object

オプション -m

m=1で実行

sam_atom_in /Input.pdb  TS
sketch_object TSH__1
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A10  A14  red
sketch_add    TS A10  A14 
end_object
sketch_object TSH__2
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A18  A35  red
sketch_add    TS A18  A35 
end_object
sketch_object TSH__3
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A51  A63  red
sketch_add    TS A51  A63 
end_object
sketch_object TSH__4
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A66  A70  red
sketch_add    TS A66  A70 
end_object
sketch_object TSH__5
sketch_setup  Spiral solid 2.5 0.5 0.5 2 7 3 2
sketch_type   Spiral
paint_zone TS A72  A81  red
sketch_add    TS A72  A81 
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

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   A10  white
sketch_add    TS A1   A10 
end_object
sketch_object TSN__2
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A14  A18  white
sketch_add    TS A14  A18 
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

-中略-

sketch_object TSN_48
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A81  A87  white
sketch_add    TS A81  A87 
end_object
sketch_object TSN_49
sketch_setup  Rattler solid 0.5 7 2
sketch_type   Rattler 
paint_zone TS A101 0   white
sketch_add    TS A101 0  
end_object