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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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