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Re: CIF: Getting a structure drawing program to create a "legal"

  • Subject: Re: CIF: Getting a structure drawing program to create a "legal"
  • From: "Herbert J. Bernstein" <yaya@xxxxxxxxxxxxxxxxxxxxxxx>
  • Date: Thu, 21 Dec 2000 02:59:51 GMT
This CIF is almost, but not quite right.  The problem is that the loop header

loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv

has 5 tags, but the table has six columns:

As1      0.17662   0.00740   0.25574   0.03748  Uani

You need to align the two either by adding the missing tag in the header, or by
dropping all the "Uani"'s.  I took out the "Uani"'s with BBEdit and the
file then loaded very nicely with RasMol 2.7.1.

  -- H. J. Bernstein

At 2:28 +0000 12/21/00, L. Cranswick wrote:
>Getting a structure drawing program to
>create a "legal" CIF?
>
>I am helping Jean Laugier add CIF exporting to
>the Gretep for Windows structure drawing software.
>(Jean received help from I.D. Brown adding CIF
>capability for importing CIF)  I am mainly
>helping out in a testing capacity.
>
>However, in trying to create a CIF file that
>programs like WinGX and Platon are happy with
>is prooving tiresome.  As we keep finding out
>by trial and error - missing keywords that
>cause the very high quality WinGX CIF importer
>to barf.
>
>Thus my query is - what extra information would
>it take before a decent CIF importer will be
>friendly to this style of file?  Example given below.
>
>(If there is not an easy answer for this - perhaps
>the crystallographic world should stick with
>Shelx INS as the defacto "standard" structure
>format for swapping structure co-ordinates
>around? )
>
>Lachlan.
>
>
>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
>_symmetry_cell_setting          Monoclinic
>loop_
>          _symmetry_equiv_pos_as_xyz
>         ' X, Y, Z'
>         '-X, Y,-Z'
>
>_symmetry_space_group_name_H-M   'P2'
>
>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
>O2       0.50880  -0.10520   0.46520   0.07791  Uani
>O1       0.27147   0.00360   0.38592   0.05589  Uani
>C1      -0.02629  -0.01908   0.25001   0.03711  Uani
>C2      -0.10283   0.01408   0.32250   0.05126  Uani
>C3      -0.24500  -0.01110   0.31769   0.05363  Uani
>H1      -0.30896   0.01625   0.37207   0.04448  Uani
>C4      -0.30577  -0.07218   0.24236   0.05925  Uani
>H2      -0.41334  -0.09514   0.24361   0.04448  Uani
>C5      -0.23042  -0.10285   0.16757   0.05068  Uani
>H3      -0.28133  -0.14520   0.10411   0.04448  Uani
>C6      -0.08808  -0.07889   0.17407   0.04644  Uani
>H4      -0.02404  -0.10664   0.12005   0.04448  Uani
>C7      -0.04095   0.08386   0.40354   0.06551  Uani
>H5       0.07017   0.09610   0.39719   0.04448  Uani
>H6      -0.04442   0.06569   0.48748   0.04448  Uani
>H7      -0.10546   0.13846   0.38250   0.04448  Uani
>C8       0.17921   0.11245   0.18458   0.04058  Uani
>C9       0.31191   0.15407   0.18933   0.04470  Uani
>C10      0.30492   0.22881   0.13389   0.06187  Uani
>H8       0.40405   0.26292   0.13627   0.04448  Uani
>C11      0.17635   0.26068   0.07643   0.07128  Uani
>H9       0.17582   0.31875   0.03434   0.04448  Uani
>C12      0.04665   0.21818   0.07214   0.06208  Uani
>H10     -0.05411   0.24320   0.02629   0.04448  Uani
>C13      0.04666   0.14440   0.12633   0.05193  Uani
>H11     -0.05370   0.11152   0.12414   0.04448  Uani
>C14      0.45386   0.12144   0.24885   0.06043  Uani
>H12      0.43721   0.06333   0.28631   0.04448  Uani
>H13      0.50236   0.16410   0.31272   0.04448  Uani
>H14      0.52524   0.11319   0.19079   0.04448  Uani
>C15      0.24851  -0.06884   0.16149   0.03690  Uani
>C16      0.26699  -0.15280   0.18685   0.04757  Uani
>C17      0.33131  -0.20210   0.11774   0.06047  Uani
>H15      0.34896  -0.26616   0.13770   0.04448  Uani
>C18      0.37263  -0.17148   0.02563   0.06679  Uani
>H16      0.41906  -0.21203  -0.02739   0.04448  Uani
>C19      0.35577  -0.08895  -0.00121   0.06178  Uani
>H17      0.38950  -0.06489  -0.07395   0.04448  Uani
>C20      0.29599  -0.03910   0.06627   0.04809  Uani
>H18      0.28418   0.02529   0.04662   0.04448  Uani
>C21      0.22012  -0.18901   0.28788   0.06713  Uani
>H19      0.17286  -0.14166   0.33079   0.04448  Uani
>H20      0.31354  -0.21468   0.34299   0.04448  Uani
>H21      0.14066  -0.23653   0.26177   0.04448  Uani
>
>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
>H1       0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C4       0.04098   0.08016   0.05257  -0.00737  -0.00416   0.02527
>H2       0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C5       0.03182   0.07202   0.04498   0.00060  -0.00066  -0.00065
>H3       0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C6       0.04664   0.05843   0.03084  -0.00116  -0.00461   0.00024
>H4       0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C7       0.06279   0.06989   0.05943  -0.00541   0.01533  -0.02607
>H5       0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>H6       0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>H7       0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>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
>H8       0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C11      0.09158   0.04880   0.06765   0.01764   0.01896   0.00918
>H9       0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C12      0.05589   0.06034   0.06532   0.00773   0.00812   0.00158
>H10      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C13      0.05461   0.05862   0.03865   0.01134  -0.00141  -0.00631
>H11      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C14      0.04238   0.08110   0.05382  -0.00524  -0.00024  -0.00229
>H12      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>H13      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>H14      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>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
>H15      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C18      0.04815   0.08821   0.05971   0.00668   0.00382  -0.02864
>H16      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C19      0.05774   0.08311   0.04075  -0.00927   0.00801  -0.01079
>H17      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C20      0.03461   0.06639   0.04034  -0.00103   0.00425  -0.00847
>H18      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>C21      0.07275   0.05886   0.06415  -0.00038   0.00100   0.01615
>H19      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>H20      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>H21      0.12814   0.00000   0.00000   0.00000   0.00000   0.00000
>
>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
>
>
>
>--
>Lachlan M. D. Cranswick
>
>Collaborative Computational Project No 14 (CCP14)
>    for Single Crystal and Powder Diffraction
>Daresbury Laboratory, Warrington, WA4 4AD U.K
>Tel: +44-1925-603703  Fax: +44-1925-603124
>E-mail: l.cranswick@dl.ac.uk  Ext: 3703  Room C14
>                           http://www.ccp14.ac.uk


=====================================================
****                BERNSTEIN + SONS
*   *       INFORMATION SYSTEMS CONSULTANTS
****     P.O. BOX 177, BELLPORT, NY 11713-0177
*   * ***
**** *            Herbert J. Bernstein
  *   ***     yaya@bernstein-plus-sons.com
 ***     *
  *   *** 1-631-286-1339    FAX: 1-631-286-1999
=====================================================



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