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RE: Getting a structure drawing program to create a "legal" CIF?

  • Subject: RE: Getting a structure drawing program to create a "legal" CIF?
  • From: "Peter Y. Zavalij" <zavalij@xxxxxxxxxxxxxx>
  • Date: Thu, 21 Dec 2000 03:33:01 GMT
Hi Lachlan,
  1st there is 6 columns but only 5 defined in the header.
loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
As1      0.17662   0.00740   0.25574   0.03748  Uani
..

The 6th column should be _atom_site_adp_type

After correction ATOMS can read data.
However, the problem (at least in PLATON) is "incorrect" ellipsoids for H
atoms.
They are claimed to be "Uani" and only U11 is not 0.
For isotropic atoms _atom_site_adp_type should be Uiso and they should not
be in
the anisoptropic list.

I would also add to the atomic table the following columns:
_atom_site_type_symbol
_atom_site_occupancy

Now, Platon works however I could not make OrtepIII work but it looks like
it is
Win2000 problem, at least I could not read other files too.

Peter Zavalij

Below is modified CIF file:
------------------------------------
data_block1
_chemical_formula_sum   'C21 H21 O2 As1'
_cell_length_a                      9.3860
_cell_length_b                     16.3360
_cell_length_c                     12.2870
_cell_angle_alpha                    90.00
_cell_angle_beta                    101.50
_cell_angle_gamma                    90.00
_cell_formula_units_Z             2

_symmetry_cell_setting            monoclinic
_symmetry_space_group_name_H-M   'P 2'

loop_
          _symmetry_equiv_pos_as_xyz
         ' x, y, z'
         '-x, y,-z'


loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
 _atom_site_occupancy
As1  As   0.17662   0.00740   0.25574   0.03748  Uani 1
O2   O    0.50880  -0.10520   0.46520   0.07791  Uani 1
O1   O    0.27147   0.00360   0.38592   0.05589  Uani 1
C1   C   -0.02629  -0.01908   0.25001   0.03711  Uani 1
C2   C   -0.10283   0.01408   0.32250   0.05126  Uani 1
C3   C   -0.24500  -0.01110   0.31769   0.05363  Uani 1
H1   H   -0.30896   0.01625   0.37207   0.04448  Uiso 1
C4   C   -0.30577  -0.07218   0.24236   0.05925  Uani 1
H2   H   -0.41334  -0.09514   0.24361   0.04448  Uiso 1
C5   C   -0.23042  -0.10285   0.16757   0.05068  Uani 1
H3   H   -0.28133  -0.14520   0.10411   0.04448  Uiso 1
C6   C   -0.08808  -0.07889   0.17407   0.04644  Uani 1
H4   H   -0.02404  -0.10664   0.12005   0.04448  Uiso 1
C7   C   -0.04095   0.08386   0.40354   0.06551  Uani 1
H5   H    0.07017   0.09610   0.39719   0.04448  Uiso 1
H6   H   -0.04442   0.06569   0.48748   0.04448  Uiso 1
H7   H   -0.10546   0.13846   0.38250   0.04448  Uiso 1
C8   C    0.17921   0.11245   0.18458   0.04058  Uani 1
C9   C    0.31191   0.15407   0.18933   0.04470  Uani 1
C10  C    0.30492   0.22881   0.13389   0.06187  Uani 1
H8   H    0.40405   0.26292   0.13627   0.04448  Uiso 1
C11  C    0.17635   0.26068   0.07643   0.07128  Uani 1
H9   H    0.17582   0.31875   0.03434   0.04448  Uiso 1
C12  C    0.04665   0.21818   0.07214   0.06208  Uani 1
H10  H   -0.05411   0.24320   0.02629   0.04448  Uiso 1
C13  C    0.04666   0.14440   0.12633   0.05193  Uani 1
H11  H   -0.05370   0.11152   0.12414   0.04448  Uiso 1
C14  C    0.45386   0.12144   0.24885   0.06043  Uani 1
H12  H    0.43721   0.06333   0.28631   0.04448  Uiso 1
H13  H    0.50236   0.16410   0.31272   0.04448  Uiso 1
H14  H    0.52524   0.11319   0.19079   0.04448  Uiso 1
C15  C    0.24851  -0.06884   0.16149   0.03690  Uani 1
C16  C    0.26699  -0.15280   0.18685   0.04757  Uani 1
C17  C    0.33131  -0.20210   0.11774   0.06047  Uani 1
H15  H    0.34896  -0.26616   0.13770   0.04448  Uiso 1
C18  C    0.37263  -0.17148   0.02563   0.06679  Uani 1
H16  H    0.41906  -0.21203  -0.02739   0.04448  Uiso 1
C19  C    0.35577  -0.08895  -0.00121   0.06178  Uani 1
H17  H    0.38950  -0.06489  -0.07395   0.04448  Uiso 1
C20  C    0.29599  -0.03910   0.06627   0.04809  Uani 1
H18  H    0.28418   0.02529   0.04662   0.04448  Uiso 1
C21  C    0.22012  -0.18901   0.28788   0.06713  Uani 1
H19  H    0.17286  -0.14166   0.33079   0.04448  Uiso 1
H20  H    0.31354  -0.21468   0.34299   0.04448  Uiso 1
H21  H    0.14066  -0.23653   0.26177   0.04448  Uiso 1

loop_
_atom_site_aniso_label
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_12
_atom_site_aniso_U_13
_atom_site_aniso_U_23
As1      0.02789   0.05069   0.03138  -0.00131  -0.00036  -0.00055
O2       0.07338   0.09415   0.06051  -0.00481  -0.00378   0.00808
O1       0.05084   0.08903   0.02400  -0.00866  -0.01715   0.00750
C1       0.02696   0.05475   0.02786   0.00602   0.01230  -0.00785
C2       0.03650   0.06045   0.05320   0.00982   0.00236   0.00990
C3       0.04122   0.07459   0.04195   0.00592   0.00729   0.00394
C4       0.04098   0.08016   0.05257  -0.00737  -0.00416   0.02527
C5       0.03182   0.07202   0.04498   0.00060  -0.00066  -0.00065
C6       0.04664   0.05843   0.03084  -0.00116  -0.00461   0.00024
C7       0.06279   0.06989   0.05943  -0.00541   0.01533  -0.02607
C8       0.03367   0.05299   0.03235  -0.00136   0.00014  -0.00232
C9       0.03035   0.05953   0.04186  -0.00356   0.01515  -0.00910
C10      0.06366   0.05241   0.06512  -0.00180   0.02204  -0.00909
C11      0.09158   0.04880   0.06765   0.01764   0.01896   0.00918
C12      0.05589   0.06034   0.06532   0.00773   0.00812   0.00158
C13      0.05461   0.05862   0.03865   0.01134  -0.00141  -0.00631
C14      0.04238   0.08110   0.05382  -0.00524  -0.00024  -0.00229
C15      0.02016   0.05225   0.03607   0.00089   0.00280   0.00026
C16      0.02945   0.05476   0.05490   0.00143  -0.00247   0.00466
C17      0.03964   0.05895   0.07773   0.01133  -0.00540  -0.00759
C18      0.04815   0.08821   0.05971   0.00668   0.00382  -0.02864
C19      0.05774   0.08311   0.04075  -0.00927   0.00801  -0.01079
C20      0.03461   0.06639   0.04034  -0.00103   0.00425  -0.00847
C21      0.07275   0.05886   0.06415  -0.00038   0.00100   0.01615

loop_
 _geom_bond_atom_site_label_1
 _geom_bond_atom_site_label_2
 _geom_bond_distance
 _geom_bond_site_symmetry_1
 _geom_bond_site_symmetry_2
As1  O1      1.669   1_555  1_555
As1  C1      1.941   1_555  1_555
As1  C8      1.928   1_555  1_555
As1  C15     1.913   1_555  1_555
C1   C2      1.363   1_555  1_555
C1   C6      1.395   1_555  1_555
C2   C3      1.386   1_555  1_555
C2   C7      1.548   1_555  1_555
C3   H1      1.080   1_555  1_555
C3   C4      1.403   1_555  1_555
C4   H2      1.080   1_555  1_555
C4   C5      1.362   1_555  1_555
C5   H3      1.080   1_555  1_555
C5   C6      1.379   1_555  1_555
C6   H4      1.080   1_555  1_555
C7   H5      1.080   1_555  1_555
C7   H6      1.080   1_555  1_555
C7   H7      1.080   1_555  1_555
C8   C9      1.410   1_555  1_555
C8   C13     1.406   1_555  1_555
C9   C10     1.393   1_555  1_555
C9   C14     1.485   1_555  1_555
C10  H8      1.080   1_555  1_555
C10  C11     1.373   1_555  1_555
C11  H9      1.080   1_555  1_555
C11  C12     1.393   1_555  1_555
C12  H10     1.080   1_555  1_555
C12  C13     1.377   1_555  1_555
C13  H11     1.080   1_555  1_555
C14  H12     1.080   1_555  1_555
C14  H13     1.080   1_555  1_555
C14  H14     1.080   1_555  1_555
C15  C16     1.410   1_555  1_555
C15  C20     1.418   1_555  1_555
C16  C17     1.392   1_555  1_555
C16  C21     1.517   1_555  1_555
C17  H15     1.080   1_555  1_555
C17  C18     1.363   1_555  1_555
C18  H16     1.080   1_555  1_555
C18  C19     1.389   1_555  1_555
C19  H17     1.080   1_555  1_555
C19  C20     1.360   1_555  1_555
C20  H18     1.080   1_555  1_555
C21  H19     1.080   1_555  1_555
C21  H20     1.080   1_555  1_555
C21  H21     1.080   1_555  1_555

loop_
 _geom_angle_atom_site_label_1
 _geom_angle_atom_site_label_2
 _geom_angle_atom_site_label_3
 _geom_angle
 _geom_angle_site_symmetry_1
 _geom_angle_site_symmetry_2
 _geom_angle_site_symmetry_3
O1   As1  C1   111.008  1_555  1_555  1_555
O1   As1  C8   114.519  1_555  1_555  1_555
O1   As1  C15  111.761  1_555  1_555  1_555
C1   As1  C8   106.435  1_555  1_555  1_555
C1   As1  C15  107.157  1_555  1_555  1_555
C8   As1  C15  105.490  1_555  1_555  1_555
C2   C1   C6   120.826  1_555  1_555  1_555
C3   C2   C7   118.705  1_555  1_555  1_555
H1   C3   C4   119.967  1_555  1_555  1_555
H2   C4   C5   119.638  1_555  1_555  1_555
H3   C5   C6   120.510  1_555  1_555  1_555
H5   C7   H6   109.471  1_555  1_555  1_555
H5   C7   H7   109.463  1_555  1_555  1_555
H6   C7   H7   109.472  1_555  1_555  1_555
C9   C8   C13  121.782  1_555  1_555  1_555
C10  C9   C14  120.362  1_555  1_555  1_555
H8   C10  C11  118.838  1_555  1_555  1_555
H9   C11  C12  119.935  1_555  1_555  1_555
H10  C12  C13  119.943  1_555  1_555  1_555
H12  C14  H13  109.475  1_555  1_555  1_555
H12  C14  H14  109.474  1_555  1_555  1_555
H13  C14  H14  109.474  1_555  1_555  1_555
C16  C15  C20  118.076  1_555  1_555  1_555
C17  C16  C21  120.342  1_555  1_555  1_555
H15  C17  C18  119.218  1_555  1_555  1_555
H16  C18  C19  119.508  1_555  1_555  1_555
H17  C19  C20  120.735  1_555  1_555  1_555
H19  C21  H20  109.461  1_555  1_555  1_555
H19  C21  H21  109.470  1_555  1_555  1_555
H20  C21  H21  109.475  1_555  1_555  1_555


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