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I previously asked a question about a CIF file here (namely CIF fields that are available for some atoms, but not others) I think I have the answer (namely to place dots [.] at places where the two missing terms would normally appear), although I felt I'd wait to see if anyone answers in case I am wrong. Presently I have this CIF file:

#=====================================================================
# X-ray crystallography data from Pharma Res, 1995
#---------------------------------------------------------------------

data_methylphenidate

_cell_length_a                9.401(3)
_cell_length_b                7.3053(7)
_cell_length_c                11.113(3)
_cell_angle_alpha             90
_cell_angle_beta              109.260(2)
_cell_angle_gamma             90
_cell_formula_units_Z         2
_cell_volume                  720.5(3)
_cell_measurement_temperature 295.15
_cell_measurement_reflns_used 1797

_chemical_formula_sum         'C14 H20 Cl N O2'
_chemical_formula_weight      269.77
_chemical_name_systematic     'methyl (2S)-2-phenyl-2-[(2S)-piperidin-2-yl]acetate;hydrochloride'
_chemical_identifier_inchi    'InChI=1S/C14H19NO2.ClH/c1-17-14(16)13(11-7-3-2-4-8-11)12-9-5-6-10-15-12;/h2-4,7-8,12-13,15H,5-6,9-10H2,1H3;1H/t12-,13-;/m0./s1'
_chemical_identifier_inchi_key 'JUMYIBMBTDDLNG-QNTKWALQSA-N'

_refine_ls_R_factor_gt        0.070

_space_group_crystal_system   monoclinic
_space_group_name_H-M_alt     'P 21'
_space_group_IT_number        4

loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
'-x, y+1/2, -z'

loop_
_atom_site_label
_atom_site_chemical_conn_number
_atom_site_cartn_x
_atom_site_cartn_y
_atom_site_cartn_z
_atom_site_adp_type
_atom_site_B_iso_or_equiv
_atom_site_type_symbol
N1   1  -0.8852(9) 0.120(1)   -1.0300(8) Biso 3.1(2)   N
H1a  2  -0.965     0.0850     -1.001     .      .      H
H1b  3  -0.880     -0.080     -1.033     .      .      H
C2   4  -0.739(1)  0.049(2)   -0.940(1)  Biso 3.9(2)   C
H2   5  -0.746     -0.080     -0.936     .      .      H
C3   6  -0.614(1)  0.092(1)   -0.988(1)  Biso 5.1(3)   C
H3a  7  -0.525     0.0380     -0.933     .      .      H
H3b  8  -0.603     0.2210     -0.990     .      .      H
C4   9  -0.640(1)  0.021(2)   -1.122(1)  Biso 5.0(3)   C
H4a  10 -0.639     -0.110     -1.119     .      .      H
H4b  11 -0.561     0.0640     -1.150     .      .      H
C5   12 -0.792(2)  0.086(1)   -1.213(1)  Biso 5.3(3)   C
H5a  13 -0.786     0.2150     -1.225     .      .      H
H5b  14 -0.812     0.0250     -1.291     .      .      H
C6   15 -0.915(1)  0.049(2)   -1.160(1)  Biso 4.3(2)   C
H6a  16 -1.004     0.1050     -1.214     .      .      H
H6b  17 -0.928     -0.080     -1.159     .      .      H
C7   18 -0.721(1)  0.124(1)   -0.809(1)  Biso 3.3(2)   C
H7   19 -0.737     0.2520     -0.817     .      .      H
C8   20 -0.834(1)  0.051(2)   -0.7527(9) Biso 3.8(2)   C
O9   21 -0.889(1)  0.172(1)   -0.6908(9) Biso 4.9(2)   O
C10  22 -0.998(2)  0.113(2)   -0.634(1)  Biso 5.8(4)   C
H10a 23 -1.028     0.2150     -0.594     .      .      H
H10b 24 -0.956     0.0210     -0.572     .      .      H
H10c 25 -1.085     0.0650     -0.698     .      .      H
C11  26 -0.563(1)  0.093(1)   -0.709(1)  Biso 3.9(3)   C
C12  27 -0.509(2)  -0.091(2)  -0.681(1)  Biso 5.6(3)   C
H12  28 -0.566     -0.192     -0.726     .      .      H
C13  29 -0.376(2)  -0.114(3)  -0.590(2)  Biso 7.2(4)   C
H13  30 -0.343     -0.238     -0.572     .      .      H
C14  31 -0.290(2)  0.009(6)   -0.522(2)  Biso 11.3(8)  C
H14  32 -0.1960    -0.018     -0.460     .      .      H
C15  33 -0.343(2)  0.204(4)   -0.548(2)  Biso 9.0(6)   C
H15  34 -0.284     0.3020     -0.501     .      .      H
C16  35 -0.479(2)  0.242(2)   -0.643(1)  Biso 5.9(3)   C
H16  36 -0.515     0.3640     -0.664     .      .      H
O3   37 -0.871(1)  -0.1124(9) -0.7590(9) Biso 5.7(2)   O
Cl   38 -0.8105(3) 0.5484     -1.0089(3) Biso 4.72(6)  Cl

. The problem is that Avogadro and enCIFer are having trouble rendering it and I don't see what the problem is. e.g., this is what Avogadro is giving me at the moment:

enter image description here

Are _cell_measurement_theta_min and _cell_measurement_theta_max the problem (namely that I haven't specified them)?

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  • $\begingroup$ I changed some lines and got it right. Can you please check it. drive.google.com/file/d/0B_uHH541lFwhS1VJcGpkQ3o4YzA/… $\endgroup$
    – Osman Mamun
    May 2, 2015 at 3:21
  • $\begingroup$ Sure did. I think I see what you did too, you changed the Beqs to 1, removed the standard deviations & conn number column and added occupancies. Did ya do anything I missed? $\endgroup$
    – Josh Pinto
    May 2, 2015 at 3:33
  • $\begingroup$ (I meant you sure got it right, Avogadro & Mercury are rendering it right.) $\endgroup$
    – Josh Pinto
    May 2, 2015 at 3:42
  • $\begingroup$ Ok, the basic change i did was, to convert cartesian coord to fractional coord system because clearly from your attached figure you can see they are all coalesced in a small area at (000), that means your position should be scaled up. $\endgroup$
    – Osman Mamun
    May 2, 2015 at 5:41

1 Answer 1

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Mamun's answer enabled me to find the fault in my CIF file. I was using cartn categories for fract data. Here's the correct file: 

#=====================================================================
# X-ray crystallography data from Pharma Res, 1995
#---------------------------------------------------------------------

data_methylphenidate

_cell_length_a                9.401(3)
_cell_length_b                7.3053(7)
_cell_length_c                11.113(3)
_cell_angle_alpha             90
_cell_angle_beta              109.260(2)
_cell_angle_gamma             90
_cell_formula_units_Z         2
_cell_volume                  720.5(3)
_cell_measurement_temperature 295.15
_cell_measurement_reflns_used 1797

_chemical_formula_sum         'C14 H20 Cl N O2'
_chemical_formula_weight      269.77
_chemical_name_systematic     'methyl (2S)-2-phenyl-2-[(2S)-piperidin-2-yl]acetate;hydrochloride'
_chemical_identifier_inchi    'InChI=1S/C14H19NO2.ClH/c1-17-14(16)13(11-7-3-2-4-8-11)12-9-5-6-10-15-12;/h2-4,7-8,12-13,15H,5-6,9-10H2,1H3;1H/t12-,13-;/m0./s1'
_chemical_identifier_inchi_key 'JUMYIBMBTDDLNG-QNTKWALQSA-N'

_refine_ls_R_factor_gt        0.070

_space_group_crystal_system   monoclinic
_space_group_name_H-M_alt     'P 21'
_space_group_IT_number        4

loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
'-x, y+1/2, -z'

loop_
_atom_site_label
_atom_site_occupancy
_atom_site_chemical_conn_number
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_adp_type
_atom_site_B_iso_or_equiv
_atom_site_type_symbol
N1   1.0  1  -0.8852(9) 0.120(1)   -1.0300(8) Biso 3.1(2)   N
H1a  1.0  2  -0.965     0.0850     -1.001     .      .      H
H1b  1.0  3  -0.880     -0.080     -1.033     .      .      H
C2   1.0  4  -0.739(1)  0.049(2)   -0.940(1)  Biso 3.9(2)   C
H2   1.0  5  -0.746     -0.080     -0.936     .      .      H
C3   1.0  6  -0.614(1)  0.092(1)   -0.988(1)  Biso 5.1(3)   C
H3a  1.0  7  -0.525     0.0380     -0.933     .      .      H
H3b  1.0  8  -0.603     0.2210     -0.990     .      .      H
C4   1.0  9  -0.640(1)  0.021(2)   -1.122(1)  Biso 5.0(3)   C
H4a  1.0  10 -0.639     -0.110     -1.119     .      .      H
H4b  1.0  11 -0.561     0.0640     -1.150     .      .      H
C5   1.0  12 -0.792(2)  0.086(1)   -1.213(1)  Biso 5.3(3)   C
H5a  1.0  13 -0.786     0.2150     -1.225     .      .      H
H5b  1.0  14 -0.812     0.0250     -1.291     .      .      H
C6   1.0  15 -0.915(1)  0.049(2)   -1.160(1)  Biso 4.3(2)   C
H6a  1.0  16 -1.004     0.1050     -1.214     .      .      H
H6b  1.0  17 -0.928     -0.080     -1.159     .      .      H
C7   1.0  18 -0.721(1)  0.124(1)   -0.809(1)  Biso 3.3(2)   C
H7   1.0  19 -0.737     0.2520     -0.817     .      .      H
C8   1.0  20 -0.834(1)  0.051(2)   -0.7527(9) Biso 3.8(2)   C
O9   1.0  21 -0.889(1)  0.172(1)   -0.6908(9) Biso 4.9(2)   O
C10  1.0  22 -0.998(2)  0.113(2)   -0.634(1)  Biso 5.8(4)   C
H10a 1.0  23 -1.028     0.2150     -0.594     .      .      H
H10b 1.0  24 -0.956     0.0210     -0.572     .      .      H
H10c 1.0  25 -1.085     0.0650     -0.698     .      .      H
C11  1.0  26 -0.563(1)  0.093(1)   -0.709(1)  Biso 3.9(3)   C
C12  1.0  27 -0.509(2)  -0.091(2)  -0.681(1)  Biso 5.6(3)   C
H12  1.0  28 -0.566     -0.192     -0.726     .      .      H
C13  1.0  29 -0.376(2)  -0.114(3)  -0.590(2)  Biso 7.2(4)   C
H13  1.0  30 -0.343     -0.238     -0.572     .      .      H
C14  1.0  31 -0.290(2)  0.009(6)   -0.522(2)  Biso 11.3(8)  C
H14  1.0  32 -0.1960    -0.018     -0.460     .      .      H
C15  1.0  33 -0.343(2)  0.204(4)   -0.548(2)  Biso 9.0(6)   C
H15  1.0  34 -0.284     0.3020     -0.501     .      .      H
C16  1.0  35 -0.479(2)  0.242(2)   -0.643(1)  Biso 5.9(3)   C
H16  1.0  36 -0.515     0.3640     -0.664     .      .      H
O3   1.0  37 -0.871(1)  -0.1124(9) -0.7590(9) Biso 5.7(2)   O
Cl   1.0  38 -0.8105(3) 0.5484     -1.0089(3) Biso 4.72(6)  Cl
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  • 1
    $\begingroup$ +1 Nicely spotted! On a very minor side note: If a very strict CIF checker complains about line length > 80 characters, as it could for the INCHI key block, you can always use a text block with ; on leading and trailing lines instead of a string in quotation marks on the same line as the _something label. This is what you typically do when submitting CIF files for publication in IUCr journals. Please have a look at DOI for further information. $\endgroup$
    – Klaus-Dieter Warzecha
    May 2, 2015 at 4:47

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