From pjuhas at bnl.gov Tue Jan 30 00:48:34 2018 From: pjuhas at bnl.gov (Pavol Juhas) Date: Mon, 29 Jan 2018 17:48:34 -0500 Subject: [Cod-bugs] fix _atom_site_aniso_label in 2003481 Message-ID: Hello, I have noticed that a test reading of entry 2003481 fails, because _atom_site_aniso_label does not match _atom_site_label. According to https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_aniso_label.html the labels should match. The enclosed patch should correct this. Best, Pavol -- Dr. Pavol Juhas Computational Science Initiative Brookhaven National Laboratory P.O. Box 5000 Upton, NY 11973-5000 tel: +1-631-344-3594 fax: +1-631-344-2739 -------------- next part -------------- From c49f7de96b82c6b10bac85ba36027a7869db215b Mon Sep 17 00:00:00 2001 From: Pavol Juhas Date: Mon, 29 Jan 2018 16:19:21 -0500 Subject: Fix _atom_site_aniso_label in 2003481 Match `_atom_site_label`. --- cif/2/00/34/2003481.cif | 84 ++++++++++++++++++++++++------------------------- 1 file changed, 42 insertions(+), 42 deletions(-) diff --git a/cif/2/00/34/2003481.cif b/cif/2/00/34/2003481.cif index b7b8f24..12b3b51 100644 --- a/cif/2/00/34/2003481.cif +++ b/cif/2/00/34/2003481.cif @@ -142,48 +142,48 @@ _atom_site_aniso_U_22 _atom_site_aniso_U_23 _atom_site_aniso_U_33 I 0.0530(2) -0.0045(2) -0.0005(2) 0.0554(3) -0.0001(2) 0.0533(2) -V1 0.0426(5) 0.0002(5) 0.0059(5) 0.0389(6) -0.0016(5) 0.0360(5) -V2 0.0402(5) 0.0014(5) -0.0002(5) 0.0357(5) -0.0004(5) 0.0398(5) -O1 0.044(2) 0.004(2) 0.010(2) 0.054(3) -0.002(2) 0.061(3) -O2 0.058(3) -0.006(2) 0.011(2) 0.060(3) -0.008(2) 0.041(2) -O3 0.060(3) 0.002(2) 0.001(2) 0.049(3) 0.010(2) 0.050(3) -O4 0.054(3) 0.002(2) 0.000(2) 0.044(2) -0.007(2) 0.046(2) -O5 0.037(2) 0.002(2) -0.000(2) 0.046(2) -0.006(2) 0.032(2) -OW1 0.078(4) 0.018(3) 0.064(6) 0.053(4) 0.042(6) 0.40(1) -OW2 0.31(1) -0.046(9) 0.04(1) 0.144(8) 0.005(8) 0.18(1) -N1 0.034(2) -0.002(2) 0.000(2) 0.035(3) -0.004(2) 0.039(3) -N2 0.042(3) 0.002(2) 0.002(2) 0.041(3) -0.000(2) 0.039(3) -N11 0.040(3) 0.004(2) 0.005(2) 0.040(3) -0.003(2) 0.041(3) -N21 0.042(3) -0.002(2) 0.005(2) 0.041(3) 0.001(2) 0.041(3) -N31 0.046(3) -0.003(3) -0.001(2) 0.044(3) 0.004(3) 0.040(3) -N41 0.048(3) 0.002(3) -0.001(2) 0.044(3) 0.002(3) 0.038(3) -C1 0.041(3) 0.002(3) -0.005(3) 0.043(3) 0.001(3) 0.044(3) -C2 0.043(3) -0.006(3) -0.002(3) 0.045(4) -0.007(3) 0.050(4) -C3 0.042(3) -0.001(3) 0.002(3) 0.044(3) -0.004(3) 0.035(3) -C4 0.042(3) 0.002(3) 0.006(3) 0.043(3) -0.005(3) 0.040(3) -C5 0.040(3) -0.000(3) 0.002(3) 0.053(4) -0.004(3) 0.038(3) -C6 0.061(4) 0.010(3) 0.003(3) 0.041(4) -0.001(3) 0.055(4) -C7 0.038(3) -0.001(3) 0.009(3) 0.060(4) -0.002(3) 0.050(4) -C11 0.034(3) 0.005(3) 0.007(3) 0.043(3) -0.000(3) 0.042(3) -C12 0.049(4) 0.006(3) 0.003(3) 0.049(4) 0.004(3) 0.054(4) -C13 0.069(4) 0.007(4) 0.010(4) 0.042(4) 0.005(4) 0.062(4) -C14 0.061(4) 0.001(4) 0.010(4) 0.046(4) -0.006(4) 0.063(4) -C15 0.046(3) 0.002(3) 0.006(3) 0.040(3) -0.005(3) 0.051(4) -C21 0.038(3) -0.005(3) 0.010(3) 0.041(3) 0.002(3) 0.051(4) -C22 0.048(3) -0.010(3) 0.012(3) 0.044(4) -0.003(3) 0.055(4) -C23 0.057(4) -0.002(3) 0.018(4) 0.042(4) 0.005(4) 0.070(4) -C24 0.058(4) -0.000(4) 0.008(4) 0.055(4) 0.016(4) 0.061(4) -C25 0.052(4) -0.002(3) 0.006(3) 0.048(4) 0.006(3) 0.048(4) -C31 0.044(3) -0.002(3) 0.003(3) 0.044(4) 0.008(3) 0.049(4) -C32 0.044(4) -0.001(4) 0.007(4) 0.065(5) 0.000(4) 0.069(5) -C33 0.048(4) -0.016(4) -0.005(4) 0.091(6) 0.007(5) 0.075(5) -C34 0.058(4) -0.012(4) -0.008(4) 0.068(5) -0.002(4) 0.062(4) -C35 0.050(4) -0.004(3) -0.006(3) 0.050(4) -0.002(3) 0.048(4) -C41 0.050(4) 0.005(3) -0.005(3) 0.042(4) -0.001(3) 0.049(4) -C42 0.123(7) 0.015(5) 0.007(5) 0.042(4) 0.005(4) 0.068(5) -C43 0.160(9) 0.007(6) -0.002(6) 0.058(5) 0.025(4) 0.067(5) -C44 0.118(7) 0.002(5) -0.005(5) 0.066(5) 0.015(4) 0.047(4) -C45 0.066(4) -0.003(4) 0.003(3) 0.055(4) 0.003(4) 0.047(4) +V(1) 0.0426(5) 0.0002(5) 0.0059(5) 0.0389(6) -0.0016(5) 0.0360(5) +V(2) 0.0402(5) 0.0014(5) -0.0002(5) 0.0357(5) -0.0004(5) 0.0398(5) +O(1) 0.044(2) 0.004(2) 0.010(2) 0.054(3) -0.002(2) 0.061(3) +O(2) 0.058(3) -0.006(2) 0.011(2) 0.060(3) -0.008(2) 0.041(2) +O(3) 0.060(3) 0.002(2) 0.001(2) 0.049(3) 0.010(2) 0.050(3) +O(4) 0.054(3) 0.002(2) 0.000(2) 0.044(2) -0.007(2) 0.046(2) +O(5) 0.037(2) 0.002(2) -0.000(2) 0.046(2) -0.006(2) 0.032(2) +O(W1) 0.078(4) 0.018(3) 0.064(6) 0.053(4) 0.042(6) 0.40(1) +O(W2) 0.31(1) -0.046(9) 0.04(1) 0.144(8) 0.005(8) 0.18(1) +N(1) 0.034(2) -0.002(2) 0.000(2) 0.035(3) -0.004(2) 0.039(3) +N(2) 0.042(3) 0.002(2) 0.002(2) 0.041(3) -0.000(2) 0.039(3) +N(11) 0.040(3) 0.004(2) 0.005(2) 0.040(3) -0.003(2) 0.041(3) +N(21) 0.042(3) -0.002(2) 0.005(2) 0.041(3) 0.001(2) 0.041(3) +N(31) 0.046(3) -0.003(3) -0.001(2) 0.044(3) 0.004(3) 0.040(3) +N(41) 0.048(3) 0.002(3) -0.001(2) 0.044(3) 0.002(3) 0.038(3) +C(1) 0.041(3) 0.002(3) -0.005(3) 0.043(3) 0.001(3) 0.044(3) +C(2) 0.043(3) -0.006(3) -0.002(3) 0.045(4) -0.007(3) 0.050(4) +C(3) 0.042(3) -0.001(3) 0.002(3) 0.044(3) -0.004(3) 0.035(3) +C(4) 0.042(3) 0.002(3) 0.006(3) 0.043(3) -0.005(3) 0.040(3) +C(5) 0.040(3) -0.000(3) 0.002(3) 0.053(4) -0.004(3) 0.038(3) +C(6) 0.061(4) 0.010(3) 0.003(3) 0.041(4) -0.001(3) 0.055(4) +C(7) 0.038(3) -0.001(3) 0.009(3) 0.060(4) -0.002(3) 0.050(4) +C(11) 0.034(3) 0.005(3) 0.007(3) 0.043(3) -0.000(3) 0.042(3) +C(12) 0.049(4) 0.006(3) 0.003(3) 0.049(4) 0.004(3) 0.054(4) +C(13) 0.069(4) 0.007(4) 0.010(4) 0.042(4) 0.005(4) 0.062(4) +C(14) 0.061(4) 0.001(4) 0.010(4) 0.046(4) -0.006(4) 0.063(4) +C(15) 0.046(3) 0.002(3) 0.006(3) 0.040(3) -0.005(3) 0.051(4) +C(21) 0.038(3) -0.005(3) 0.010(3) 0.041(3) 0.002(3) 0.051(4) +C(22) 0.048(3) -0.010(3) 0.012(3) 0.044(4) -0.003(3) 0.055(4) +C(23) 0.057(4) -0.002(3) 0.018(4) 0.042(4) 0.005(4) 0.070(4) +C(24) 0.058(4) -0.000(4) 0.008(4) 0.055(4) 0.016(4) 0.061(4) +C(25) 0.052(4) -0.002(3) 0.006(3) 0.048(4) 0.006(3) 0.048(4) +C(31) 0.044(3) -0.002(3) 0.003(3) 0.044(4) 0.008(3) 0.049(4) +C(32) 0.044(4) -0.001(4) 0.007(4) 0.065(5) 0.000(4) 0.069(5) +C(33) 0.048(4) -0.016(4) -0.005(4) 0.091(6) 0.007(5) 0.075(5) +C(34) 0.058(4) -0.012(4) -0.008(4) 0.068(5) -0.002(4) 0.062(4) +C(35) 0.050(4) -0.004(3) -0.006(3) 0.050(4) -0.002(3) 0.048(4) +C(41) 0.050(4) 0.005(3) -0.005(3) 0.042(4) -0.001(3) 0.049(4) +C(42) 0.123(7) 0.015(5) 0.007(5) 0.042(4) 0.005(4) 0.068(5) +C(43) 0.160(9) 0.007(6) -0.002(6) 0.058(5) 0.025(4) 0.067(5) +C(44) 0.118(7) 0.002(5) -0.005(5) 0.066(5) 0.015(4) 0.047(4) +C(45) 0.066(4) -0.003(4) 0.003(3) 0.055(4) 0.003(4) 0.047(4) loop_ _atom_site_label _atom_site_fract_x -- 2.16.0 From antanas.vaitkus90 at gmail.com Tue Jan 30 11:32:45 2018 From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus) Date: Tue, 30 Jan 2018 11:32:45 +0200 Subject: [Cod-bugs] fix _atom_site_aniso_label in 2003481 In-Reply-To: References: Message-ID: Dear Pavol Juhas, thank You for the bug report. I have corrected the entry in question. Generally, we are aware of validation errors like these (we have the software to diagnose it), but we simply lack manpower to correct it all at once. As such, we have to prioritize. If You encounter similar mislabeling problems in the future, feel free to send us a list of files that affect Your work the most and we will try to address them ASAP. Sincerely, Antanas Vaitkus 2018-01-30 0:48 GMT+02:00 Pavol Juhas : > Hello, > > I have noticed that a test reading of entry 2003481 fails, because > _atom_site_aniso_label does not match _atom_site_label. According to > https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core. > dic/Iatom_site_aniso_label.html > the labels should match. The enclosed patch should correct this. > > Best, > > Pavol > > -- > Dr. Pavol Juhas > Computational Science Initiative > Brookhaven National Laboratory > P.O. Box 5000 > Upton, NY 11973-5000 > tel: +1-631-344-3594 > fax: +1-631-344-2739 > > _______________________________________________ > Cod-bugs mailing list > Cod-bugs at lists.crystallography.net > http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs > > -- Antanas Vaitkus, PhD student at Vilnius University Institute of Biotechnology, room V325, Saul?tekio al. 7, LT-10257 Vilnius, Lithuania -------------- next part -------------- An HTML attachment was scrubbed... URL: From nbehrnd at yahoo.com Tue Jan 30 17:26:01 2018 From: nbehrnd at yahoo.com (Behrnd Norwid) Date: Tue, 30 Jan 2018 15:26:01 +0000 (UTC) Subject: [Cod-bugs] "crystal structure alarm" / feature suggestion References: <340292280.4944757.1517325961835.ref@mail.yahoo.com> Message-ID: <340292280.4944757.1517325961835@mail.yahoo.com> ??????? Dear developers and maintainers of COD, ??? the other day I set an alarm in Thomson-Reuter's / Clarivate's literature data base Web of Science, i.e. periodically, the data base will check if an article interesting for me was cited by an other publication, and inform me -- even if the result shall be ``none'' (when the data base is not aware about a recent additional citation of this work). ??? From this experience, on one side, and remembering that at least a considerable fraction of the data deposited in the COD may be retrieved by pattern comparison of Smiles which in turn may be automated, the thought occured to me that something similar might be implemented in the COD's portfolio.? There are two kind of alerts I am aware of: + The COD user wants to stay abreast about the discovery of new polymorphs of organic molecules, with models already curated in the COD.? This may be of interest for pharmacological relevant ingredients since at least some of the exhibit different physicochemical / pharmacocinetical properties and are patented / deplyed as "polymorph A" rather than "polymorph B". + To the astonishment of a COD user, there is a gap -- a crystalline compound was not yet characterized by diffraction analysis, or at least, COD is not (yet) aware of such a data set.? Beside the option to perform this characterization by himself / herself, s/he might be interested to learn when this characterization was done by someone else; and subsequently access the original publication COD points to. ??? While I do not assume, that this list of reasons for such an alert is exhaustive, the two perspectives are appealing enough to suggest such an implementation in crystallographic data bases, too.? Provided COD is updated much more frequently than CCDC's CSD file, perhaps the implementation shows of benefits earlier, than at CCDC to which I wrote, too.? From which specialty within chemistry COD receives the most data per unit of time?? This likely different ratio might contribute to determine if such crawling across the newly curated data shall be performed monthly, quarterly, once a year.? On the other hand, maybe the task is facilitated because COD is backed by subversion; and the repeatitive crawling "just" has to be told to go back in history to the date of the last crawl per profile (in other words, commit #212121), instead of digesting all folder and data again. ??? With kind regards, Norwid Behrnd, PhD | | Virenfrei. www.avg.com | -------------- next part -------------- An HTML attachment was scrubbed... URL: