sortatom.exe
SHELXS outputs the structure solution in the res file. The atoms are aligned in the peak height, but its order is different from the chemical numbering. For the numbering, the atoms are re-arranged along the chemical bonds from the start atom. The start atom is inputed or chosen the one of two atoms having the longest distance in the structure.
2015.1.27

Program：sortatom.exe.zip (Windows/32bit)   /  sortatom.zip (OSX10.7/Intel i5)

Input eg: test1.res

Output eg1: test1a.res   auto arrange
Output eg1: test1b.res   from the strat atom

＊Download from the right-click menu.


Input

test1.res :
The coorinates with SHELX format. The early structure of cyclic decapetpide Tyrocidine-B c[Val-Orn(OBzl)-Leu-DPhe-Pro-Trp-DPhe-Asn-Gln-Phe]. 

   TITL Tyrocidine-B(Z) P212121
   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
   TEMP -173
   C001  1  0.43620   0.55638   0.46053   11.000   0.05  99.00 
   C002  1  0.44997   0.77481   0.61016   11.000   0.05  91.17 
   C003  1  0.53326   1.09592   0.58496   11.000   0.05  90.35 
   C004  1  0.44117   0.65702   0.49400   11.000   0.05  88.21 
   C005  1  0.50497   0.98884   0.59736   11.000   0.05  86.49 
   C006  1  0.44501   0.90630   0.63609   11.000   0.05  83.58 
   C007  1  0.44795   0.63107   0.54113   11.000   0.05  81.95 
   ...

　　　
　　　Mercury showing.

The return code of Windows is different from OSX. OSX file has CR, but this return code does not work for OSX programs. Please change CR to LF (Linux) or CR+LF (win).


Usage

SHELXS outputs test1.res with the peaks height order. WInGX or Mercury shows the molecular structure.

For numbering test1.res with the chemical structure, the peaks height order forces the huge patient. 

   1    2        3    4   5   6   7    8   9   10
c[Val-Orn(OBzl)-Leu-DPhe-Pro-Trp-DPhe-Asn-Gln-Phe]

  C001   ---> D-Phe7 C = C072
  C002   ---> Gln9 N   = N091
  C003   ---> Phe10 Cα = C101
  C004   ---> Asn8 N   = N081
  ...
Numbring like the blue letters, and re-arranege the atoms along the chemical bonds.

プログラムもデータも同じフォルダーに保存します。
　　　

meibomatch.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。

自動並べ替え（分子構造の一番端を起点にした並べ替え） 

         SORT atoms array along structure
         ================================

 Input RES/INS file: test1.res   ← 入力


 Output file: test1a.res   ← 出力

  >> Read   97 atoms

 Need atom-list? [Y/N*]:  ［リターン］

 :: SORTING from 
    [*Cr] THE ATOM HAVING THE LONGEST VECTOR FROM CENTER
      [2] INPUT ATOM

  Which ?:   ［リターン］
                ↑ これで2原子の組合せの中で最も距離が長い2原子を選び、
                  どちらか一方を並び替えの先頭にもってくる

  >> SORT started at: C001  

  >> Remaining  2 atoms are NOT devided to any fragment.
     These atoms have no fragment number.
      ↑ 結合を調べたところ、2つの原子がどのクラスターにも属さない

   ------- OK? : 

  >> SORT started at: C054  ← C054を結合のスタート原子に設定


    Job finshed. OK?


結果1
test1a.res の座標はC054（上図Mercuryの表示を参照）から、結合可能原子が順に並ぶ。その選び方にルールはないので、原子のリスト順は化学的なナンバリングと必ずしも一致しない。 

   TITL Tyrocidine-B(Z) P212121
   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   0                                                     ↓ クラスタ番号
   C054     1   0.60204   0.92606   0.77591   11.00   0.05000   1
   C024     1   0.59653   0.94390   0.73219   11.00   0.05000   1
   C025     1   0.59546   0.83680   0.70070   11.00   0.05000   1
   C038     1   0.59319   1.08381   0.71896   11.00   0.05000   1
   C045     1   0.58760   0.86173   0.65593   11.00   0.05000   1
   C048     1   0.58644   1.10231   0.67361   11.00   0.05000   1
   C015     1   0.58342   1.00083   0.64022   11.00   0.05000   1
   C019     1   0.57614   1.04045   0.59036   11.00   0.05000   1
   C003     1   0.53326   1.09592   0.58496   11.00   0.05000   1
   C005     1   0.50497   0.98884   0.59736   11.00   0.05000   1
   ....


基点を指定して並べ替え 
         SORT atoms array along structure
         ================================

 Input RES/INS file: test1.res

 Output file: test1b.res

  >> Read   97 atoms

 Need atom-list? [Y/N*]: ［リターン］

 :: SORTING from 
    [*Cr] THE ATOM HAVING THE LONGEST VECTOR FROM CENTER
      [2] INPUT ATOM

  Which ?:  2     ← 基点原子入力を選択

   ------- OK? : 

  :: ATOMS of FRAGMENT 1
     C001  C004  C009  C039  C007  C017  C040  C013  C032  C027  
     C026  C002  C011  C022  C029  C047  C042  C044  C006  C031  
     C051  C014  C036  C064  C052  C028  C046  C075  C041  C049  
     C005  C034  C012  C073  C088  C055  C072  C003  C008  C062  
     C085  C074  C078  C081  C019  C021  C020  C023  C063  C066  
     C067  C089  C092  C015  C018  C035  C056  C080  C094  C045  
     C048  C010  C069  C079  C025  C038  C016  C033  C058  C077  
     C024  C030  C037  C065  C068  C043  C050  C070  C087  C054  
     C059  C053  C086  C071  C082  C057  C084  C091  C076  C060  
     C097  C090  C093  C096  C095  

    INPUT START ATOM ([Cr]=Atom having the LONGEST vector): C018
     原子名は大文字小文字も区別される。もし、一致する原子名がないと自動選択に戻る。
  >> SORT started at: C018  
   > This fragment has  95 atoms 
     C018  C021  C010  C003  C035  C016  C033  C005  C019  C030  
     C037  C065  C068  C028  C015  C059  C006  C034  C045  C048  
     C057  C084  C002  C046  C025  C038  C053  C060  C097  C013  
     C012  C024  C050  C096  C007  C011  C008  C054  C058  C086  
     C095  C004  C032  C020  C023  C069  C043  C091  C001  C022  
     C056  C090  C093  C009  C039  C031  C051  C066  C079  C017  
     C040  C062  C080  C077  C027  C026  C073  C063  C070  C087  
     C029  C047  C042  C044  C075  C085  C067  C071  C082  C014  
     C036  C064  C052  C088  C076  C041  C049  C055  C072  C074  
     C078  C081  C089  C092  C094  
   > REMAINING:   2 ATOMS

    Job finshed. OK?


結果2
test1b.res の座標はC018（上図Mercuryの表示を参照：N(Val1)）から、結合可能原子が順に並ぶ。その選び方にルールはないので、原子のリスト順は化学的なナンバリングと必ずしも一致しない。 

   TITL Tyrocidine-B(Z) P212121
   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   0     
   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
   C016     1   0.46333   1.06097   0.44595   11.00   0.05000   1
   C033     1   0.53524   1.09180   0.42778   11.00   0.05000   1
   C005     1   0.50497   0.98884   0.59736   11.00   0.05000   1
   C019     1   0.57614   1.04045   0.59036   11.00   0.05000   1
   C030     1   0.43025   1.13344   0.43789   11.00   0.05000   1
   C037     1   0.45863   0.91801   0.44269   11.00   0.05000   1
   ....


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