Convert CIF file to SDF file using free Linux-compatible software other than Avogadro or OpenBabel?

Question

I am trying to convert http://crystallography.net/cod/2236556.cif to a file that I can open in Avogadro without some bonds disappearing. See this crystal structure is of tianeptine hydrochloride, yet many of the bonds are not shown when I open the CIF in Avogadro.

This is what the CIF is meant to be rendered like (shown in PyMOL):

while this is what I see in Avogadro (also displayed like this in Avogadro 2):

note how so many bonds are not shown properly. I suspect if I could convert the molecule to SDF or CML or some other 3D chemical format I'd be able to fix this issue and Avogadro will be able to render the file properly.

I have tried doing the file conversion with OpenBabel but the files generated look, when viewed in PyMOL or Jmol (which render the CIF fine), just like the CIF does in Avogadro with all the disconnected atoms.

Answer 1

It seems like OpenBabel and Avogadro sometimes don't ideally parse certain CIF-files' connectivity data. As OP mentioned, PyMOL and other crystallographically-oriented programs (I personally like Olex2, it also run under Linux and is free) do it on-the-fly:

As @GeoffHutchison suggested in a similar thread on binding atoms within a unit cell, Mercury does a good job at providing MOL/SDF files from CIF data. As of now, there is an installation script for Linux for Mercury 3.9. Avogadro handles such MOL file from Mercury way better:

2236556
  --CCDC--071617    3D                              

 56 57  0  0  0  0  0  0  0  0999 V2000
    1.3664    7.7013    4.0020 Cl     0
    6.6663    8.7266    4.4355 S      0
    6.1525    9.4153    5.5710 O      0
    7.7255    7.7726    4.6043 O      0
    4.7213    0.8967    7.6943 O      0
    2.6223    1.3499    8.2786 O      0
    2.9354    1.3046    9.0347 H      0
    7.1953    9.8372    3.3639 N      0
    7.6456    5.9591    2.4701 N      0
    8.4385    5.8198    2.0682 H      0
    7.8134    6.2148    3.3161 H      0
    5.3238    7.9653    3.5835 C      0
    4.0381    8.0880    4.1077 C      0
    3.8953    8.5011    4.9288 H      0
    2.9772    7.5765    3.3740 C      0
    3.1781    6.9816    2.1438 C      0
    2.4563    6.6559    1.6556 H      0
    4.4680    6.8774    1.6459 C      0
    4.6013    6.4768    0.8168 H      0
    5.5699    7.3547    2.3503 C      0
    6.9378    7.0993    1.7546 C      0
    6.7575    6.7565    0.8547 H      0
    7.9197    8.2523    1.5451 C      0
    8.8050    8.0470    0.4790 C      0
    8.7594    7.2477    0.0049 H      0
    9.7458    8.9915    0.1090 C      0
   10.3266    8.8270   -0.5988 H      0
    9.8106   10.1839    0.8033 C      0
   10.4293   10.8326    0.5572 H      0
    8.9631   10.4081    1.8540 C      0
    9.0175   11.2135    2.3156 H      0
    8.0176    9.4560    2.2492 C      0
    6.3410   11.0331    3.1948 C      0
    6.8195   11.7005    2.6977 H      0
    6.1061   11.3837    4.0569 H      0
    5.5420   10.7916    2.7197 H      0
    6.8948    4.6534    2.5072 C      0
    7.5354    3.9263    2.4577 H      0
    6.3296    4.5991    1.7205 H      0
    6.0338    4.4553    3.7359 C      0
    5.2898    5.0768    3.7165 H      0
    6.5567    4.6337    4.5332 H      0
    5.5123    3.0333    3.7738 C      0
    5.0259    2.8601    2.9524 H      0
    6.2680    2.4268    3.8010 H      0
    4.6053    2.7307    4.9451 C      0
    3.8347    3.3179    4.9116 H      0
    5.0816    2.9111    5.7713 H      0
    4.1326    1.2872    4.9481 C      0
    4.8942    0.7100    5.1149 H      0
    3.7873    1.0713    4.0679 H      0
    3.0575    0.9929    5.9842 C      0
    2.3293    1.6247    5.8729 H      0
    2.7039    0.1030    5.8300 H      0
    3.5713    1.0798    7.3895 C      0
    6.3200    5.1537   -1.1307 Cl     0
  1 15  1
  2  3  1
  2  4  1
  2  8  1
  2 12  1
  5 55  1
  6  7  1
  6 55  1
  8 32  1
  8 33  1
  9 10  1
  9 11  1
  9 21  1
  9 37  1
 12 13  1
 12 20  1
 13 14  1
 13 15  1
 15 16  1
 16 17  1
 16 18  1
 18 19  1
 18 20  1
 20 21  1
 21 22  1
 21 23  1
 23 24  1
 23 32  1
 24 25  1
 24 26  1
 26 27  1
 26 28  1
 28 29  1
 28 30  1
 30 31  1
 30 32  1
 33 34  1
 33 35  1
 33 36  1
 37 38  1
 37 39  1
 37 40  1
 40 41  1
 40 42  1
 40 43  1
 43 44  1
 43 45  1
 43 46  1
 46 47  1
 46 48  1
 46 49  1
 49 50  1
 49 51  1
 49 52  1
 52 53  1
 52 54  1
 52 55  1
M  END
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