expdbins.exe
座標変換 PDB→SHELX、または SHELX→PDBを行います。
2015.2.4

プログラム:expdbins.exe.zip (Windows)  /   expdbins.zip (OSX10.7)

入力データ例:test1b.ins (SHELX format)

出力データ例:test1b2.pdb (PDB format)

*ダウンロードは 右クリック して「リンク先を保存」などを選んで下さい。入力・出力例はテキストなので、メモ帳などで開くことができます。


SHELX insとres

   TITL Tyrocidine-B(Z) P212121
   REM   c[Val-Orn-Leu-D-Phe-Pro-Tyr-Gln-Asn-D-Phe-Trp]
   CELL  0.836  34.1331   9.5394  30.2385  90.000  90.000  90.000
   ZERR   4.00   0.0068   0.0019   0.0060   0.000   0.000   0.000
   LATT  -1
   SYMM  0.5-X,-Y,0.5+Z
   SYMM  0.5+X,0.5-Y,-Z
   SYMM  -X,0.5+Y,0.5-Z
   SFAC  C H N O
   UNIT  272 352 56 52
   RESI   1  TTY      ← 残基番号と残基名
   C018     1   0.50674   1.07911   0.50833   11.00   0.05000   1
   C021     1   0.52722   1.14772   0.53826   11.00   0.05000   1
   C010     1   0.49905   1.12708   0.46133   11.00   0.05000   1
   C003     1   0.53326   1.09592   0.58496   11.00   0.05000   1
   C035     1   0.54418   1.26727   0.52441   11.00   0.05000   1
   ...

使い方

プログラムもデータも同じフォルダーに保存します。expdbins.exeをダブルクリックすると、MS-DOSのコマンドプロンプトが現れます。

あとは必要なデータを入力します。入力は部分は赤色です。

         Exchange Format between PDB and INS files
          This is an expart namer for oligopeptide



 Input PDB/INS file: test1b.ins
 INPUT> File format was SHELXS/L

 Put Uij (ANISOU) into PDB [Y/*N]: [return]
 SHELX=  Tyrocidine-B(Z) P212121   ← SHELXデータと判断
 SHELX= REM   c[Val-Orn-Leu-D-Phe-Pro-Tyr-Gln-Asn-D-Phe-Trp]
 SHELX= CELL  0.836  34.1331   9.5394  30.2385  90.000  90.000  90.000
 SHELX= ZERR   4.00   0.0068   0.0019   0.0060   0.000   0.000   0.000
 SHELX= LATT  -1
 SHELX= SYMM  0.5-X,-Y,0.5+Z
 SHELX= SYMM  0.5+X,0.5-Y,-Z
 SHELX= SYMM  -X,0.5+Y,0.5-Z
 SHELX= SFAC  C H N O
 SHELX= UNIT  272 352 56 52

 NATOM> Read   97 atoms

 REMA> TITL Tyrocidine-B(Z) P212121|REM    c[Val-Orn-Leu-D-Phe-Pro-Tyr-Gln-Asn-
 REMA> D-Phe-Trp]|CELL   0.836  34.1331   9.5394  30.2385  90.000  90.000  90.0
 REMA> 00|ZERR    4.00   0.0068   0.0019   0.0060   0.000   0.000   0.000|LATT 
 REMA>   -1|SYMM   0.5-X,-Y,0.5+Z|SYMM   0.5+X,0.5-Y,-Z|SYMM   -X,0.5+Y,0.5-Z|S
 REMA> FAC   C H N O|UNIT   272 352 56 52
 CELL>     34.133     9.539    30.239    90.000    90.000    90.000

 Remove hydrogens [Y/*N]: [return]

 SPACE GROUP: [return]

 Put CONECT informations to PDB [y/*n]: [return]

 Output file name: test1b.pdb     ← 拡張子がinsからpdbに変更


   Job finshed. OK? 



test1b.pdb

HEADER File converted at             Input SHELXS/L INS file: test1b.pdb       
EXPDTA    X-Ray diffraction
REMA TITL Tyrocidine-B(Z) P212121
REMA REM    c[Val-Orn-Leu-D-Phe-Pro-Tyr-Gln-Asn-D-Phe-Trp]
REMA CELL   0.836  34.1331   9.5394  30.2385  90.000  90.000  90.000
REMA ZERR    4.00   0.0068   0.0019   0.0060   0.000   0.000   0.000
REMA LATT   -1
REMA SYMM   0.5-X,-Y,0.5+Z
REMA SYMM   0.5+X,0.5-Y,-Z
REMA SYMM   -X,0.5+Y,0.5-Z
REMA SFAC   C H N O
REMA UNIT   272 352 56 52
REMA                ↑ PDB→INS変換のためのSHELX dataをヘッダーに書き込む 
CRYST1   34.133    9.539   30.239  90.00  90.00  90.00 P 1           4
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.029297  0.000000  0.000000        0.00000
SCALE2     -0.000000  0.104828  0.000000        0.00000
SCALE3      0.000000 -0.000000  0.033070        0.00000
ATOM      1 C018 TTY     1      17.297  10.294  15.371  1.00  3.95
ATOM      2 C021 TTY     1      17.996  10.949  16.276  1.00  3.95
ATOM      3 C010 TTY     1      17.034  10.752  13.950  1.00  3.95
ATOM      4 C003 TTY     1      18.202  10.454  17.688  1.00  3.95
ATOM      5 C035 TTY     1      18.575  12.089  15.857  1.00  3.95
ATOM      6 C016 TTY     1      15.815  10.121  13.485  1.00  3.95
ATOM      7 C033 TTY     1      18.269  10.415  12.935  1.00  3.95
...
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