Cod-users

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6 discussions

Re: [Cod-users] sample cif files
by Saulius Gražulis 26 Jan '17

26 Jan '17

Dear Dr. Masami Kanzaki, thank you very much for your contribution to COD! On 2017-01-26 01:29, Masami wrote:On 2017-01-26 01:29, Masami wrote: > I deposited 3.49 GPa file as well as other two files of > higher pressure without encountering the error. Wonderful, great news! I can confirm that the files are in the database as expected. > I have several other failed files, but I know how to > edit previously deposited cif, so I will add proper tags to > these files, and deposit failed files again by myself. This should work. If you edit the previously deposited files via the Web interface http://www.crystallography.net/cod, using the "Manage depositions" and then "View your depositions" links, then you should be able to update the deposited structures, adding the _diffrn_ambient_pressure data item, and after that all new depositions should succeed. > Thank you so much. Don't mention! > Masami Kanzaki Sincerely yours, Saulius >> >> Dear Dr. Masami Kanzaki, >> >> thank you very much for your information, and your great contribution to >> COD! >> >> On 2017-01-25 10:08, Masami wrote: >>> I attached two cif files. >>> "stishovite-2.96GPa.cif” was already deposited to COD (as 1544734.cif). >>> I can not deposit "stishovite-3.49GPa.cif”, and get >>> an error message shown below. >>> “The file [stishovite-3.49GPa.cif] has (at least some) structures that have been deposited to COD previously in entries >>> 1544734” >>> >>> Actually I deposited 7 cif stishovite files of 1bar, 0.95, 1.99, 2.96, 3.49, 4.55 and 5.17 GPa, >>> and only the cif of 3.49 GPa got the error message, and apparently pressure >>> difference is smallest for this pair (2.96 and 3.49 GPa). >> >> I have looked at the files you have send me and found your deposited >> structures in the COD. There reason of the error message is the following: >> >> The deposited structure files did not have the _diffrn_ambient_pressure >> data item in them. Their unit cells, however, were different enough (at >> least one cell parameter difference was outside the 3*sigma range of the >> square-added standard deviations of the respective cell parameters), so >> they all were deposited as different structures. The last structure >> (stishovite-3.49GPa.cif), however, did not experience that much change >> in the unit cell compared to the stishovite-2.96GPa.cif file. Since the >> pressure was not specified in the deposited structure, the new structure >> was caught as a duplicate. Adding pressure to just the new structure did >> not help, because the deposited 2.96 GPa structure had no pressure value >> to compare against, and thus signalled the duplicate anyway. >> >> I took my liberty to insert the _diffrn_ambient_pressure values into >> your deposited structures, taking the pressure values from the title and >> the mineral name. They now all have their measurement pressure recognised: >> >>> saulius@koala Masami Kanzaki/ > codslave 'select file, formula, a, b, c, diffrpressure/1E6 as P, mineral from data where title like "%The crystal structure of stishovite under pressure%"' >>> +---------+-----------+--------+--------+--------+--------+------------------------+ >>> | file | formula | a | b | c | P | mineral | >>> +---------+-----------+--------+--------+--------+--------+------------------------+ >>> | 1544731 | - O2 Si - | 4.1797 | 4.1797 | 2.6669 | 0.0001 | stishovite at 1bar | >>> | 1544732 | - O2 Si - | 4.1738 | 4.1738 | 2.6663 | 0.95 | stishovite at 0.95 GPa | >>> | 1544733 | - O2 Si - | 4.1693 | 4.1693 | 2.6652 | 1.99 | stishovite at 1.99 GPa | >>> | 1544734 | - O2 Si - | 4.1642 | 4.1642 | 2.6636 | 2.96 | stishovite at 2.96 GPa | >>> | 1544735 | - O2 Si - | 4.1564 | 4.1564 | 2.6602 | 4.55 | stishovite at 4.55 GPa | >>> | 1544736 | - O2 Si - | 4.152 | 4.152 | 2.659 | 5.17 | stishovite at 5.17 GPa | >>> +---------+-----------+--------+--------+--------+--------+------------------------+ >> >> You should now be able to deposit your last file, >> stishovite-3.49GPa.cif, without a problem. Could you please check if >> this is the case? If there are still error messages, please let me know, >> I'll investigate further. >> >> Sincerely yours, >> Saulius >> >> -- >> Dr. Saulius Gražulis >> Vilnius University Institute of Biotechnology, Saulėtekio al. 7 >> LT-10223 Vilnius, Lietuva (Lithuania) >> fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353 >> mobile: (+370-684)-49802, (+370-614)-36366 > -- Dr. Saulius Gražulis Vilnius University Institute of Biotechnology, Saulėtekio al. 7 LT-10223 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353 mobile: (+370-684)-49802, (+370-614)-36366

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Re: [Cod-users] deposition problem
by xtal 25 Jan '17

25 Jan '17

Dear All, Another kind of problem concerning the series of entries COD6****** These are not containing atomic coordinates such as this short one (deposited long ago as REF files... by me I think...) : #------------------------------------------------------------------------------ #$Date: 2012-02-28 12:14:52 +0000 (Tue, 28 Feb 2012) $ #$Revision: 35911 $ #$URL: file:///home/coder/svn-repositories/cod/cif/6/00/06/6000685.cif $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/ # # All data on this site have been placed in the public domain by the # contributors. # data_6000685 loop_ _publ_author_name 'Laval, J. P.' 'Champarnaudmesjard, J. C.' 'Frit, B.' 'Britel, A.' 'Mikou, A.' _publ_section_title ; BI7F11O5 - a new ordered anion-excess fluorite-related structure with columnar clusters ; _journal_name_full 'European Journal Of Solid State And Inorganic Chemistry' _journal_page_first 943 _journal_page_last 956 _journal_volume 31 _journal_year 1994 _chemical_formula_sum 'Bi7 F11 O5' _space_group_name_H-M_alt 'C 1 2 1' _cell_angle_alpha 90.000 _cell_angle_beta 96.171 _cell_angle_gamma 90.000 _cell_length_a 13.5238 _cell_length_b 5.5285 _cell_length_c 9.1886 _cell_volume 683.02 _[local]_cod_text ; LAVAL JP; CHAMPARNAUDMESJARD JC; FRIT B; BRITEL A; MIKOU A - BI7F11O5 - A NEW ORDERED ANION-EXCESS FLUORITE-RELATED STRUCTURE WITH COLUMNAR CLUSTERS - EUROPEAN JOURNAL OF SOLID STATE AND INORGANIC CHEMISTRY 31 (1994) 943-956 ; loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z ? ? ? ? _cod_database_code 6000685 Trying to deposit a CIF containing the lacking atomic coordinates, like the following, fails because it is considered as a duplicate : data_Bi7F11O5 loop_ _publ_author_name 'Laval, J.-P.' 'Champarnaud-Mesjard, J.-C.' 'Frit, B.' 'Britel, A.' 'Mikou, A.' _publ_section_title ; BI7F11O5 - a new ordered anion-excess fluorite-related structure with columnar clusters ; _journal_name_full 'European Journal of Solid State and Inorganic Chemistry' _journal_page_first 943 _journal_page_last 956 _journal_volume 31 _journal_year 1994 _chemical_formula_sum 'Bi7 F11 O5' _chemical_formula_weight 1751.86 _chemical_compound_source 'to replace COD6000685 without atomic coordinates' loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source Bi Bi -4.0111 8.9310 ' International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' F F 0.0727 0.0534 ' International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' O O 0.0492 0.0322 ' International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' _symmetry_cell_setting monoclinic _symmetry_space_group_name_Hall 'C 2y' _symmetry_space_group_name_H-M 'C 2' _symmetry_Int_Tables_number 5 loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 x,y,z 2 -x,y,-z 3 1/2+x,1/2+y,z 4 1/2-x,1/2+y,-z _cell_length_a 13.5238(3) _cell_length_b 5.5285(1) _cell_length_c 9.1886(2) _cell_angle_alpha 90 _cell_angle_beta 96.171(1) _cell_angle_gamma 90 _cell_formula_units_Z 2 _cell_volume 683.02(2) _exptl_crystal_density_diffrn 8.518 _exptl_crystal_density_meas 8.65 _exptl_crystal_F_000 1440 _exptl_absorpt_coefficient_mu 174.841 _diffrn_radiation_type CuK\a _diffrn_radiation_wavelength 1.54184 _diffrn_radiation_probe 'x-ray' _diffrn_ambient_temperature 293 _refine_ls_number_parameters 46 _pd_proc_ls_prof_R_factor 0.050 _pd_proc_ls_prof_wR_factor 0.068 _refine_ls_R_I_factor 0.033 _cod_depositor_comments ; Rietveld refinements, software Fullprof ; loop_ _atom_site_label _atom_site_type_symbol _atom_site_thermal_displace_type _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_occupancy _atom_site_U_iso_or_equiv _atom_site_calc_flag _atom_site_refinement_flags _atom_site_disorder_assembly _atom_site_disorder_group Bi1 Bi Uiso 0.5689(2) 0.00000 0.2129(4) 1.000 0.100(10) . . . . Bi2 Bi Uiso 0.3061(3) -0.0130(10) 0.3604(5) 1.000 0.100(10) . . . . Bi3 Bi Uiso 0.00000 0.8966(9) 0.50000 1.000 0.100(10) . . . . Bi4 Bi Uiso 0.8742(3) 0.9148(8) 0.0792(5) 1.000 0.100(10) . . . . F1 F Uiso 0.00000 0.217(13) 0.00000 1.000 1.1(3) . . . . F2 F Uiso 0.447(3) 0.710(10) 0.285(5) 1.000 1.1(3) . . . . F3 F Uiso 0.319(3) 0.632(6) 0.517(4) 1.000 1.1(3) . . . . F4 F Uiso 0.695(3) 0.071(7) 0.946(5) 1.000 1.1(3) . . . . F5 F Uiso 0.641(3) 0.390(6) 0.203(5) 1.000 1.1(3) . . . . F6 F Uiso 0.255(3) 0.383(7) 0.267(5) 1.000 1.1(3) . . . . O1 O Uiso 0.00000 0.636(10) 0.00000 1.000 0.4(6) . . . . O2 O Uiso 0.424(3) 0.205(8) 0.270(5) 1.000 0.4(6) . . . . O3 O Uiso 0.601(3) 0.120(6) 0.458(4) 1.000 0.4(6) . . . . 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 _geom_bond_publ_flag Bi1 F5 2.37(3) . . yes Bi1 O2 2.37(4) . . yes Bi1 O3 2.34(4) . . yes Bi1 F2 2.44(5) . 1_545 yes Bi1 F1 2.60(4) . 3_545 yes Bi1 F6 2.59(4) . 3_545 yes Bi1 O1 2.21(2) . 3_545 yes Bi2 F6 2.43(4) . . yes Bi2 O2 2.23(4) . . yes Bi2 F2 2.60(5) . 1_545 yes Bi2 F3 2.43(3) . 1_545 yes Bi2 O3 2.11(4) . 2_656 yes Bi2 F5 2.58(4) . 3_445 yes Bi2 F3 2.28(4) . 4_546 yes Bi3 F2 2.67(5) . 3_455 yes Bi3 O2 2.49(4) . 3_455 yes Bi3 O3 2.11(4) . 3_455 yes Bi3 F2 2.67(5) . 4_556 yes Bi3 O2 2.49(5) . 4_556 yes Bi3 O3 2.11(4) . 4_556 yes Bi4 F4 2.74(4) . 1_564 yes Bi4 O1 2.46(3) . 1_655 yes Bi4 F1 2.55(5) . 1_665 yes Bi4 F2 2.61(5) . 3_555 yes Bi4 F6 2.49(4) . 3_555 yes Bi4 O2 2.15(5) . 3_555 yes Bi4 F5 2.58(5) . 4_655 yes Bi4 F4 2.12(4) . 4_656 yes 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 _geom_angle_publ_flag F5 Bi1 O2 85.8(14) . . . yes F5 Bi1 O3 75.2(14) . . . yes F2 Bi1 F5 154.1(16) 1_545 . . yes F1 Bi1 F5 129.4(16) 3_545 . . yes F5 Bi1 F6 80.8(13) . . 3_545 yes F5 Bi1 O1 78.0(16) . . 3_545 yes O2 Bi1 O3 74.0(15) . . . yes F2 Bi1 O2 69.9(16) 1_545 . . yes F1 Bi1 O2 102.5(12) 3_545 . . yes F6 Bi1 O2 152.2(15) 3_545 . . yes O1 Bi1 O2 75.7(12) 3_545 . . yes F2 Bi1 O3 89.2(14) 1_545 . . yes F1 Bi1 O3 155.3(13) 3_545 . . yes F6 Bi1 O3 79.1(14) 3_545 . . yes O1 Bi1 O3 140.6(15) 3_545 . . yes F1 Bi1 F2 67.1(13) 3_545 . 1_545 yes F2 Bi1 F6 117.0(14) 1_545 . 3_545 yes F2 Bi1 O1 103.4(14) 1_545 . 3_545 yes F1 Bi1 F6 104.8(12) 3_545 . 3_545 yes F1 Bi1 O1 57.0(19) 3_545 . 3_545 yes F6 Bi1 O1 124.3(10) 3_545 . 3_545 yes F6 Bi2 O2 64.4(15) . . . yes F2 Bi2 F6 128.9(15) 1_545 . . yes F3 Bi2 F6 159.9(14) 1_545 . . yes F6 Bi2 O3 95.1(14) . . 2_656 yes F5 Bi2 F6 78.1(13) 3_445 . . yes F3 Bi2 F6 70.0(13) 4_546 . . yes F2 Bi2 O2 69.2(16) 1_545 . . yes F3 Bi2 O2 130.5(15) 1_545 . . yes O2 Bi2 O3 73.6(16) . . 2_656 yes F5 Bi2 O2 120.9(15) 3_445 . . yes F3 Bi2 O2 126.4(14) 4_546 . . yes F2 Bi2 F3 70.9(14) 1_545 . 1_545 yes F2 Bi2 O3 91.4(14) 1_545 . 2_656 yes F2 Bi2 F5 110.1(13) 1_545 . 3_445 yes F2 Bi2 F3 161.0(14) 1_545 . 4_546 yes F3 Bi2 O3 79.3(13) 1_545 . 2_656 yes F3 Bi2 F5 99.6(12) 1_545 . 3_445 yes F3 Bi2 F3 90.1(13) 1_545 . 4_546 yes F5 Bi2 O3 157.0(14) 3_445 . 2_656 yes F3 Bi2 O3 84.1(14) 4_546 . 2_656 yes F3 Bi2 F5 72.9(13) 4_546 . 3_445 yes F2 Bi3 O2 66.0(15) 3_455 . 3_455 yes F2 Bi3 O3 117.5(14) 3_455 . 3_455 yes F2 Bi3 F2 99.0(16) 3_455 . 4_556 yes F2 Bi3 O2 163.8(15) 3_455 . 4_556 yes F2 Bi3 O3 118.5(14) 3_455 . 4_556 yes O2 Bi3 O3 75.7(14) 3_455 . 3_455 yes F2 Bi3 O2 163.8(15) 4_556 . 3_455 yes O2 Bi3 O2 129.6(15) 3_455 . 4_556 yes O2 Bi3 O3 68.3(14) 3_455 . 4_556 yes F2 Bi3 O3 118.5(14) 4_556 . 3_455 yes O2 Bi3 O3 68.3(14) 4_556 . 3_455 yes O3 Bi3 O3 87.3(14) 3_455 . 4_556 yes F2 Bi3 O2 66.0(15) 4_556 . 4_556 yes F2 Bi3 O3 117.5(14) 4_556 . 4_556 yes O2 Bi3 O3 75.7(14) 4_556 . 4_556 yes F4 Bi4 O1 132.3(9) 1_564 . 1_655 yes F1 Bi4 F4 104.6(12) 1_665 . 1_564 yes F2 Bi4 F4 112.0(13) 3_555 . 1_564 yes F4 Bi4 F6 74.0(14) 1_564 . 3_555 yes F4 Bi4 O2 136.1(14) 1_564 . 3_555 yes F4 Bi4 F5 66.2(13) 1_564 . 4_655 yes F4 Bi4 F4 82.8(14) 1_564 . 4_656 yes F1 Bi4 O1 79.8(16) 1_665 . 1_655 yes F2 Bi4 O1 112.8(11) 3_555 . 1_655 yes F6 Bi4 O1 132.8(13) 3_555 . 1_655 yes O1 Bi4 O2 74.8(13) 1_655 . 3_555 yes F5 Bi4 O1 69.7(9) 4_655 . 1_655 yes F4 Bi4 O1 73.6(15) 4_656 . 1_655 yes F1 Bi4 F2 65.5(12) 1_665 . 3_555 yes F1 Bi4 F6 138.3(14) 1_665 . 3_555 yes F1 Bi4 O2 115.3(12) 1_665 . 3_555 yes F1 Bi4 F5 74.4(9) 1_665 . 4_655 yes F1 Bi4 F4 149.1(16) 1_665 . 4_656 yes F2 Bi4 F6 76.4(13) 3_555 . 3_555 yes F2 Bi4 O2 71.7(16) 3_555 . 3_555 yes F2 Bi4 F5 138.1(13) 3_555 . 4_655 yes F2 Bi4 F4 140.1(16) 3_555 . 4_656 yes F6 Bi4 O2 64.3(15) 3_555 . 3_555 yes F5 Bi4 F6 134.8(14) 4_655 . 3_555 yes F4 Bi4 F6 72.6(15) 4_656 . 3_555 yes F5 Bi4 O2 140.8(14) 4_655 . 3_555 yes F4 Bi4 O2 72.6(17) 4_656 . 3_555 yes F4 Bi4 F5 81.7(15) 4_656 . 4_655 yes Bi4 F1 Bi4 98(2) 1_445 . 2_645 yes Bi1 F1 Bi4 112.1(2) 3_455 . 1_445 yes Bi1 F1 Bi4 114.4(2) 4_555 . 1_445 yes Bi1 F1 Bi4 114.4(2) 3_455 . 2_645 yes Bi1 F1 Bi4 112.1(2) 4_555 . 2_645 yes Bi1 F1 Bi1 106(3) 3_455 . 4_555 yes Bi1 F2 Bi2 103(2) 1_565 . 1_565 yes Bi1 F2 Bi4 115.3(17) 1_565 . 3_445 yes Bi1 F2 Bi3 119.5(16) 1_565 . 3_545 yes Bi2 F2 Bi4 109.4(15) 1_565 . 3_445 yes Bi2 F2 Bi3 109.4(16) 1_565 . 3_545 yes Bi3 F2 Bi4 100.4(18) 3_545 . 3_445 yes Bi2 F3 Bi2 124.6(17) 1_565 . 4_556 yes Bi4 F4 Bi4 133.7(18) 1_546 . 4_646 yes Bi1 F5 Bi2 120.1(16) . . 3_555 yes Bi1 F5 Bi4 95.6(14) . . 4_645 yes Bi2 F5 Bi4 121.5(16) 3_555 . 4_645 yes Bi2 F6 Bi4 97.4(14) . . 3_445 yes Bi1 F6 Bi2 121.8(16) 3_455 . . yes Bi1 F6 Bi4 122.4(18) 3_455 . 3_445 yes Bi4 O1 Bi4 103(2) 1_455 . 2_655 yes Bi1 O1 Bi4 101.0(5) 3_455 . 1_455 yes Bi1 O1 Bi4 103.7(5) 4_555 . 1_455 yes Bi1 O1 Bi4 103.7(5) 3_455 . 2_655 yes Bi1 O1 Bi4 101.0(5) 4_555 . 2_655 yes Bi1 O1 Bi1 140(3) 3_455 . 4_555 yes Bi1 O2 Bi2 117.7(19) . . . yes Bi1 O2 Bi4 105.8(18) . . 3_445 yes Bi1 O2 Bi3 96.7(15) . . 3_545 yes Bi2 O2 Bi4 115.0(18) . . 3_445 yes Bi2 O2 Bi3 99.2(17) . . 3_545 yes Bi3 O2 Bi4 121.9(19) 3_545 . 3_445 yes Bi1 O3 Bi2 134.0(17) . . 2_656 yes Bi1 O3 Bi3 108.9(16) . . 3_545 yes Bi2 O3 Bi3 116.7(17) 2_656 . 3_545 yes loop_ _geom_torsion_atom_site_label_1 _geom_torsion_atom_site_label_2 _geom_torsion_atom_site_label_3 _geom_torsion_atom_site_label_4 _geom_torsion _geom_torsion_site_symmetry_1 _geom_torsion_site_symmetry_2 _geom_torsion_site_symmetry_3 _geom_torsion_site_symmetry_4 _geom_torsion_publ_flag O2 Bi1 F5 Bi2 125(2) . . . 3_555 no O2 Bi1 F5 Bi4 -103.1(15) . . . 4_645 no O3 Bi1 F5 Bi2 50.8(19) . . . 3_555 no O3 Bi1 F5 Bi4 -177.7(16) . . . 4_645 no F2 Bi1 F5 Bi2 106(3) 1_545 . . 3_555 no F2 Bi1 F5 Bi4 -123(3) 1_545 . . 4_645 no F6 Bi1 F5 Bi2 -30.3(19) 3_545 . . 3_555 no F6 Bi1 F5 Bi4 101.3(14) 3_545 . . 4_645 no F5 Bi1 O2 Bi2 -165(2) . . . . no F5 Bi1 O2 Bi4 64.9(18) . . . 3_445 no F5 Bi1 O2 Bi3 -61.0(16) . . . 3_545 no O3 Bi1 O2 Bi2 -89(2) . . . . no O3 Bi1 O2 Bi4 141(2) . . . 3_445 no O3 Bi1 O2 Bi3 14.8(12) . . . 3_545 no F2 Bi1 O2 Bi2 5.9(19) 1_545 . . . no F2 Bi1 O2 Bi4 -124(2) 1_545 . . 3_445 no F1 Bi1 O2 Bi2 66(2) 3_545 . . . no F6 Bi1 O2 Bi2 -104(3) 3_545 . . . no F6 Bi1 O2 Bi4 126(3) 3_545 . . 3_445 no O1 Bi1 O2 Bi2 116(2) 3_545 . . . no F5 Bi1 O3 Bi2 -117(3) . . . 2_656 no F5 Bi1 O3 Bi3 71.4(16) . . . 3_545 no O2 Bi1 O3 Bi2 154(3) . . . 2_656 no O2 Bi1 O3 Bi3 -18.4(16) . . . 3_545 no F2 Bi1 O3 Bi2 84(3) 1_545 . . 2_656 no F6 Bi1 O3 Bi2 -33(2) 3_545 . . 2_656 no F5 Bi1 F2 Bi2 16(4) . . 1_545 . no O2 Bi1 F2 Bi2 -4.6(15) . . 1_545 . no O3 Bi1 F2 Bi2 68.7(16) . . 1_545 . no F6 Bi1 F2 Bi2 146.0(14) 3_545 . 1_545 . no F5 Bi1 F6 Bi4 -68.6(19) . . 3_545 1_545 no F5 Bi1 F6 Bi2 167(2) . . 3_545 3_545 no O2 Bi1 F6 Bi4 -131(3) . . 3_545 1_545 no O2 Bi1 F6 Bi2 104(3) . . 3_545 3_545 no O3 Bi1 F6 Bi4 -145(2) . . 3_545 1_545 no O3 Bi1 F6 Bi2 90(2) . . 3_545 3_545 no O2 Bi2 F6 Bi4 28.9(15) . . . 3_445 no O2 Bi2 F6 Bi1 165(3) . . . 3_455 no F2 Bi2 F6 Bi4 2(2) 1_545 . . 3_445 no F2 Bi2 F6 Bi1 137.8(19) 1_545 . . 3_455 no F3 Bi2 F6 Bi4 171(3) 1_545 . . 3_445 no F3 Bi2 F6 Bi1 -54(5) 1_545 . . 3_455 no O3 Bi2 F6 Bi4 98.0(16) 2_656 . . 3_445 no O3 Bi2 F6 Bi1 -126(2) 2_656 . . 3_455 no F5 Bi2 F6 Bi4 -104.2(16) 3_445 . . 3_445 no F5 Bi2 F6 Bi1 31.5(19) 3_445 . . 3_455 no F3 Bi2 F6 Bi4 179.8(18) 4_546 . . 3_445 no F3 Bi2 F6 Bi1 -44.5(19) 4_546 . . 3_455 no F6 Bi2 O2 Bi1 -163(3) . . . . no F6 Bi2 O2 Bi4 -37.8(18) . . . 3_445 no F6 Bi2 O2 Bi3 94.0(18) . . . 3_545 no F2 Bi2 O2 Bi1 -5.5(18) 1_545 . . . no F2 Bi2 O2 Bi4 120(2) 1_545 . . 3_445 no F3 Bi2 O2 Bi1 33(3) 1_545 . . . no F3 Bi2 O2 Bi4 158.5(15) 1_545 . . 3_445 no O3 Bi2 O2 Bi1 93(2) 2_656 . . . no O3 Bi2 O2 Bi4 -142(2) 2_656 . . 3_445 no F5 Bi2 O2 Bi1 -107(2) 3_445 . . . no F5 Bi2 O2 Bi4 19(3) 3_445 . . 3_445 no F3 Bi2 O2 Bi1 162.0(16) 4_546 . . . no F3 Bi2 O2 Bi4 -72(3) 4_546 . . 3_445 no F6 Bi2 F2 Bi1 31(2) . . 1_545 . no O2 Bi2 F2 Bi1 4.9(16) . . 1_545 . no F3 Bi2 F2 Bi1 -145.1(19) 1_545 . 1_545 . no O3 Bi2 F2 Bi1 -67.0(16) 2_656 . 1_545 . no F5 Bi2 F2 Bi1 121.4(15) 3_445 . 1_545 . no F6 Bi2 F3 Bi2 33(5) . . 1_545 4_546 no O2 Bi2 F3 Bi2 165.2(18) . . 1_545 4_546 no F6 Bi2 O3 Bi1 140(2) . . 2_656 2_656 no O2 Bi2 O3 Bi1 -158(3) . . 2_656 2_656 no F6 Bi2 F5 Bi4 70.1(17) . . 3_445 2_645 no F6 Bi2 F5 Bi1 -171(2) . . 3_445 3_445 no O2 Bi2 F5 Bi4 20(2) . . 3_445 2_645 no O2 Bi2 F5 Bi1 139(2) . . 3_445 3_445 no F6 Bi2 F3 Bi2 -65.0(19) . . 4_546 4_556 no O2 Bi2 F3 Bi2 -32(3) . . 4_546 4_556 no So, maybe the restriction about duplicates should not apply to the COD6****** series ? Thanks ! Armel Le Bail

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deposition problem
by Masami 24 Jan '17

24 Jan '17

Dear all, From last October, I have been depositing crystal structure data to COD picked up from mineralogy and ceramics journals published in Japan. I will continue, but I have a problem for deposition. Quite often, mineralogy papers contain a series of structural data of single sample with different pressure or temperature conditions. When depositing these data (first one of the series is fine, but for following data), I have an error message saying that there is already same data, and I can not proceed. I noticed that not all data have this problem, but when temperature or pressure difference is small from previously deposited one. I suppose criteria to identify as same data is rather loose. I tried to explicitly include “_diffrn_ambient_temperature" or “_diffrn_ambient_pressure" tag, but no effect. Is there any trick to avoid this problem? Thank you in advance. Masami Kanzaki Institute for Planetary Materials Okayama University Japan

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Test message
by Saulius Gražulis 17 May '13

17 May '13

This is a test message for testing the cod-users(a)lists.crystallography.net mailing list. -- Dr. Saulius Gražulis Vilnius University Institute of Biotechnology, Graiciuno 8 LT-02241 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556 mobile: (+370-684)-49802, (+370-614)-36366

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molecules-in-COD
by Paul Emsley 31 May '12

31 May '12

Hi, Where is there documentation about what is in molecules-in-COD? Cheers, Paul.

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Re: [Cod-users] Specifying values 'less than something' in CIFs?
by Saulius Grazulis 29 Apr '12

29 Apr '12

Hi, Peter, more detailed data curation discussion below: On 04/29/2012 02:11 PM, Peter Murray-Rust wrote: > Clearly, the value has incorrect ESU syntax, but it has slipped through > all syntax and semantics checks until now, and would probably go > unnoticed by many programs that only take numeric value but do not use > ESU. And those that interpret ESU would either report an error or, even > worse, yield unpredictable and possibly incorrect results. And we do not > know this until we run that specific program on the specific CIF. > > Yes - my JUMBOConverter system will do something similar. May I have a look at it and/or use it? > b) make software that detects and, when possible, corrects the most > common 'mistakes'; e.g. it is probably safe to change '100C' to '373.15' > (Kelvins), with a benign warning (COD deposition tools do this on > the fly). > > This is really difficult. I don't like changing things and certainly not > without metadata. Maybe an additional local COD_ field that gives the > heuristic value. That way we don't corrupt the past but also allow > people to search and compute on "better" information I have given some thought to this, and I hope our treatment of data is fair and careful enough (but comments are welcome): what we do is: a) when changing a data value, in a way which we assume is unambiguous and straightforward, we leave _cod_depositor_comments describing the change; this is done automatically for automatic changes and we also have the same policy for manual changes. b) all our data are versioned in a Subversion repository; thus, all changes can be tracked back, reviewed and reverted if necessary. c) I keep track of original data file names and blocks. While in theory ambiguous, in practice in nearly always permits to track down the original file that was used for COD deposition. We also keep original submitted files in a separate file tree/repository. Thus, we can always track back the provenance of the data. Given this, I think it is more important to have reasonably correct data ready for automatic processing, rather than to record every aberration possible. > What about adding the field: > > COD_diffrn_standards_decay_% '<1' > > and removing the old old. Removal of an invalid field is better than > throwing away the whole CIF (which is the only logical approach to error). > For anything that is understood by us humans as "room temperature" (RT, > "room temp.", "ambient temp.", etc.), we assume that the average is > meant to be 22 deg. C (comfort level in a lab), and the uncertainty to > be +/- 2 degrees (assuming it is unlikely that human crystallographers > would measure above 28 degrees C or below 16 degrees, yielding a 60% > (1*sigma) confidence interval of 2 degrees, on a broader side), ending > up with a "justified wild guess" of 295(2) (Kelvins). > > Again - convert to > COD_temperature... I have considered this approach, but I find it awkward. The reason is that any processor that will try to extract, say, temperature from a CIF will naturally process the _diffrn_ambient_temperature data item. If this is unreadable, it will (should?) report an error. If we now move these values to _cod_diffrn_ambient_temperature, we will have a large number of tags that would contain essentially the same information -- AMCSD would need to introduce _amcsd_diffrn_ambient_temperature if using the same approach, CrystalEye (when providing for me files autoconverted from ChemML :) would use something like _crystaleye_diffrn_ambient_temperature ... The list of data names is open, so no software will catch up. In addition, the values are by definition *not* conforming to the value syntax/semantics, so what do you do with them? I guess such values are useless in general. So we end up essentially deleting data, which is however correct from a human point of view (and authors might understandably be upset with this, arguing "well, don't you guys understand what '100 degrees C' means?!"). So my approach is the following. When I can reasonably *derive* a correct value, I put this derived value into the cif_core data item; e.g. we restore _diffrn_ambient_temperature value as we think the author has intended to publish it, and we use the IUCr CIF requirements for its syntax. We then invent, if necessary, a _cod_original_diffrn_ambient_temperature data item, described in cif_cod.dic (http://www.crystallography.net/cif/dictionaries/cif_cod.dic), that contains the *original* value verbatim; this value is present only when the original value was different from what we have have now in the COD CIF. This policy is implemented in full for the _cell_volume data item. The _cell_volume contains volumes computed from the cell constants in COD CIFs. If the original value was different, it is left copied to the _cod_original_cell_volume. The same is for _symmetry_space_group_name_* tags. In this way, you can process COD CIFs assuming that all values are obtained in a uniform way, and satisfy invariants that COD ensures. If you have doubt whether the values are OK, or if you want to find out whether and how they were changed, you can consult the corresponding _cod_original_... value -- and this can be done automatically. For the temperature values, we have rather a human readable _cod_depositor_comment message describing the change. But now that I am writing you this text, I realise that we should have _cod_original_... data items for temperature values as well, in a machine-readable form. Since all our data changes are versioned and all original files are tracked, I hope there will be no serious problems to assure reliable data and to establish data provenance. Regards, Saulius -- Dr. Saulius Gražulis Institute of Biotechnology, Graiciuno 8 LT-02241 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556 mobile: (+370-684)-49802, (+370-614)-36366

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