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