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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: "Frances C. Bernstein" <fcb@xxxxxxxxxxxxxxxxxxxxxxx>
  • Date: Fri, 22 Dec 2000 02:36:28 GMT
Dear Lachlan,

     I took your cif and sent it through the IUCr checkcif
protocol.  The loop with the wrong number of items in the
list yielded an error message:

TYPE_101  Alert A _atom_site_fract_x is not of type numb.

because it assumed that the loop contained repeats of five
items and it checked the type of information in the field
against the dictionary.

     You might find it useful to check your test cifs by
e-mailing them to checkcif@iucr.org (without any signature
block).

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

On Thu, 21 Dec 2000, 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
>
>

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