From kom at eqchem.s.u-tokyo.ac.jp Mon Mar 21 04:20:13 2022 From: kom at eqchem.s.u-tokyo.ac.jp (Kazuki Komatsu) Date: Mon, 21 Mar 2022 11:20:13 +0900 Subject: [Cod-bugs] COD duplication error Message-ID: Dear COD developer team, I recently try to deposit the attached cif file to the COD. It is validated, but can not be allocated as a new entry due to the duplication to the previously deposited item 1538611. The previous entry is the same compound, based on the same data from the same publication, but refined as a different structure model, so that they should be separately regarded. Could you let me know how this should be resolved? Thank you so much for your effort to manage this issue in advance. Best regards, Kazuki Komatsu, Ph.D. Associate Prof. Graduate School of Science, The University of Tokyo -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- data_iceVII_Jorgensen1985_split loop_ _publ_author_name 'Jorgensen, J. D.' 'Worlton, T. G.' _publ_section_title ; Disordered structure of D2O ice VII from in situ neutron powder diffraction ; _journal_name_full 'The Journal of Chemical Physics' _journal_year 1985 _journal_volume 83 _journal_page_first 329 _chemical_name_systematic 'Ice VII' _chemical_formula_sum 'D2 O1' _cell_length_a 3.3501(1) _cell_length_b 3.3501 _cell_length_c 3.3501 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_volume 37.60(1) _cell_formula_units_Z 2 _symmetry_space_group_name_H-M 'P n -3 m Z' _symmetry_Int_Tables_number 224 _symmetry_cell_setting cubic loop_ _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 '-y, x+1/2, z+1/2' 2 'y+1/2, x+1/2, -z' 3 'y+1/2, -x, z+1/2' 4 '-y, -x, -z' 5 '-z, x+1/2, y+1/2' 6 'z+1/2, x+1/2, -y' 7 'z+1/2, -x, y+1/2' 8 '-z, -x, -y' 9 'z+1/2, -y, x+1/2' 10 '-z, y+1/2, x+1/2' 11 'z+1/2, y+1/2, -x' 12 '-z, -y, -x' 13 'y+1/2, -z, x+1/2' 14 '-y, z+1/2, x+1/2' 15 'y+1/2, z+1/2, -x' 16 '-y, -z, -x' 17 'x+1/2, z+1/2, -y' 18 'x+1/2, -z, y+1/2' 19 '-x, z+1/2, y+1/2' 20 '-x, -z, -y' 21 'x+1/2, y+1/2, -z' 22 'x+1/2, -y, z+1/2' 23 '-x, y+1/2, z+1/2' 24 '-x, -y, -z' 25 'y, -x+1/2, -z+1/2' 26 '-y+1/2, -x+1/2, z' 27 '-y+1/2, x, -z+1/2' 28 'y, x, z' 29 'z, -x+1/2, -y+1/2' 30 '-z+1/2, -x+1/2, y' 31 '-z+1/2, x, -y+1/2' 32 'z, x, y' 33 '-z+1/2, y, -x+1/2' 34 'z, -y+1/2, -x+1/2' 35 '-z+1/2, -y+1/2, x' 36 'z, y, x' 37 '-y+1/2, z, -x+1/2' 38 'y, -z+1/2, -x+1/2' 39 '-y+1/2, -z+1/2, x' 40 'y, z, x' 41 '-x+1/2, -z+1/2, y' 42 '-x+1/2, z, -y+1/2' 43 'x, -z+1/2, -y+1/2' 44 'x, z, y' 45 '-x+1/2, -y+1/2, z' 46 '-x+1/2, y, -z+1/2' 47 'x, -y+1/2, -z+1/2' 48 '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_B_iso_or_equiv D1 D 0.433(1) 0.433(1) 0.373(2) 1.82(7) O1 O 0.25 0.25 0.25 2.14(6) From antanas.vaitkus90 at gmail.com Fri Mar 25 14:16:46 2022 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Fri, 25 Mar 2022 14:16:46 +0200 Subject: [Cod-bugs] COD duplication error In-Reply-To: References: Message-ID: Dear Kazuki Komatsu, You very correctly identified that the issue arose due to the fact that both models were derived from the same data and are therefore very similar. In the COD we handle such situations by declaring one of the structures as optimal and the rest of them (in case there is more than one alternative model) as suboptimal. The optimal structure is mainly chosen based on the R factor. In your specific case the problem could be circumvented by adding the following extra line to the CIF file that you are trying to deposit: _cod_suboptimal_structure yes This simply declares that the deposited structure is suboptimal and therefore can match a similar structure that is already in the COD. After your deposition, we will further investigate the structure to evaluate if it is actually suboptimal or optimal in regards to the existing COD structure and update the relationships accordingly. After this, the relationship will also become visible on the COD website. See COD entry 2100860 [1] for an example of how this looks (entry is marked as a suboptimal structure of COD entry 2100858). Could you please try the suggested approach and let me know if it was successful? [1] https://www.crystallography.net/cod/2100860.html Sincerely, Antanas On Mon, 21 Mar 2022 at 08:31, Kazuki Komatsu wrote: > Dear COD developer team, > > I recently try to deposit the attached cif file to the COD. It is > validated, but can not be allocated as a new entry due to the duplication > to the previously deposited item 1538611. > > The previous entry is the same compound, based on the same data from the > same publication, but refined as a different structure model, so that they > should be separately regarded. > > Could you let me know how this should be resolved? > > Thank you so much for your effort to manage this issue in advance. > > > Best regards, > > > Kazuki Komatsu, Ph.D. > > Associate Prof. > Graduate School of Science, The University of Tokyo > > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > _______________________________________________ > Cod-bugs mailing list > Cod-bugs at lists.crystallography.net > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs > -- Antanas Vaitkus, Vilnius University, Life Sciences Center, Institute of Biotechnology, room C521, Saul?tekio al. 7, LT-10257 Vilnius, Lithuania -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From kom at eqchem.s.u-tokyo.ac.jp Sat Mar 26 15:49:14 2022 From: kom at eqchem.s.u-tokyo.ac.jp (Kazuki Komatsu) Date: Sat, 26 Mar 2022 22:49:14 +0900 Subject: [Cod-bugs] COD duplication error In-Reply-To: References: Message-ID: Dear Antanas, Many thanks for your advise for sorting out my problem. I managed to deposite with the code of suboptional? as you suggested (it is once rejected, probably _cod_suboptimal_structure was automatically deleted? In the edit section, I added the code again and finally accepted) , and successfully allocated as entries 1566716. Thank you again for your kind advise, and appreciate for your effort to manage this great database! Best regards, Komatsu Antanas Vaitkus wrote on 2022/03/25 21:16: > Dear Kazuki Komatsu, > > You very correctly identified that the issue arose due to the fact > that both models were derived from the same data and are therefore > very similar. In the COD we handle such situations by declaring one of > the structures as optimal and the rest of them (in case there is more > than one alternative model) as suboptimal. The optimal structure is > mainly chosen based on the R factor. > > In your specific case the problem could be circumvented? by adding the > following extra line to the CIF file that you are trying to deposit: > > _cod_suboptimal_structure ? ? ? ?yes > > This simply declares that the deposited structure is suboptimal and > therefore can match a similar structure that is already in the COD. > After your deposition, we will further investigate the structure to > evaluate if it is actually suboptimal or optimal in regards to the > existing COD structure and update the relationships accordingly. After > this, the relationship will also become visible on the COD website. > See COD entry 2100860 [1] for an example of how this looks (entry is > marked as a suboptimal structure of COD entry 2100858). > > Could you please try the suggested approach and let me know if it was > successful? > > [1] https://www.crystallography.net/cod/2100860.html > > Sincerely, > Antanas > > > > On Mon, 21 Mar 2022 at 08:31, Kazuki Komatsu > wrote: > > Dear COD developer team, > > I recently try to deposit the attached cif file to the COD. It is > validated, but can not be allocated as a new entry due to the > duplication to the previously deposited item 1538611. > > The previous entry is the same compound, based on the same data > from the same publication, but refined as a different structure > model, so that they should be separately regarded. > > Could you let me know how this should be resolved? > > Thank you so much for your effort to manage this issue in advance. > > > Best regards, > > > Kazuki Komatsu, Ph.D. > > Associate Prof. > Graduate School of Science, The University of Tokyo > > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , > and is > believed to be clean. > _______________________________________________ > Cod-bugs mailing list > Cod-bugs at lists.crystallography.net > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs > > > > -- > Antanas Vaitkus, > Vilnius University, > Life Sciences Center, > Institute of Biotechnology, > room C521, Saul?tekio al. 7, > LT-10257 Vilnius, Lithuania > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... 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