From lortegas at pucp.edu.pe Tue Dec 5 04:27:31 2017 From: lortegas at pucp.edu.pe (Luis Ortega San Martin) Date: Mon, 4 Dec 2017 21:27:31 -0500 Subject: [Cod-bugs] Errors with files 6000694 and 6000695 Message-ID: <3e48a001-23b7-6e97-2243-00b37755cee5@pucp.edu.pe> Dear Sir/madam, I am a regular user of COD database and I have just found two cif files with errors: 6000694 and 6000695 do not contain any atoms inside. I hope you can correct this. Best regards and congratulations for this great page. Luis -- Dr. Luis Ortega San Martin Dpto. Ciencias, Secci?n Quimica Pontificia Universidad Cat?lica del Peru Av. Universitaria, 1801. San Miguel Lima 32. Peru Tlf: +511 626 2000 ext.4227 alternative e-mail: luis.ortegasm at gmail.com http://www.pucp.edu.pe/profesor/luis-ortega-san-martin/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From grazulis at ibt.lt Tue Dec 5 09:13:21 2017 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Tue, 5 Dec 2017 09:13:21 +0200 Subject: [Cod-bugs] Errors with files 6000694 and 6000695 In-Reply-To: <3e48a001-23b7-6e97-2243-00b37755cee5@pucp.edu.pe> References: <3e48a001-23b7-6e97-2243-00b37755cee5@pucp.edu.pe> Message-ID: <0927188a-9816-f616-b469-12e7c27b872c@ibt.lt> Dear Luis, thank you for your message! On 2017-12-05 04:27, Luis Ortega San Martin wrote: > I am a regular user of COD database and I have just found two cif files > with errors: 6000694 > and 6000695 do not contain any atoms inside. > > I hope you can correct this. The absence of coordinates is actually not a bug but a feature. COD stores as much information as we can get from published sources, and for some entries coordinates were not available at the point of deposition. There are more entries like this in COD; you can select them (or filter them out) using the SQL database table `data` column 'flags', e.g.: > saulius at koala ~/ $ mysql -u cod_reader -h sql.crystallography.net cod -e 'select count(*) from data where flags not like "%has coordinates%"' > +----------+ > | count(*) | > +----------+ > | 1375 | > +----------+ or by analysing _atom_site_fract_x, ..._y and ..._z data items (they contain special CIF values '?'). In due time, we hope to get all original publications for these structures and deposit the coordinates, but this is done on the best effort basis. You can help to improve COD if you have access to (some) of these publications and can send us the atomic coordinates, preferably in CIF format. Sincerely yours, Saulius -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353 mobile: (+370-684)-49802, (+370-614)-36366 From lortegas at pucp.edu.pe Tue Dec 5 15:13:44 2017 From: lortegas at pucp.edu.pe (Luis Ortega San Martin) Date: Tue, 5 Dec 2017 08:13:44 -0500 Subject: [Cod-bugs] Errors with files 6000694 and 6000695 In-Reply-To: <0927188a-9816-f616-b469-12e7c27b872c@ibt.lt> References: <3e48a001-23b7-6e97-2243-00b37755cee5@pucp.edu.pe> <0927188a-9816-f616-b469-12e7c27b872c@ibt.lt> Message-ID: Dear Saulius, Thanks for the rapid response and recommendations. If I can get the structure of these two compounds I will send you the full CIF. Thanks again Luis El 05/12/2017 a las 2:13, Saulius Gra?ulis escribi?: > Dear Luis, > > thank you for your message! > > On 2017-12-05 04:27, Luis Ortega San Martin wrote: >> I am a regular user of COD database and I have just found two cif files >> with errors: 6000694 >> and 6000695 do not contain any atoms inside. >> >> I hope you can correct this. > The absence of coordinates is actually not a bug but a feature. COD > stores as much information as we can get from published sources, and for > some entries coordinates were not available at the point of deposition. > There are more entries like this in COD; you can select them (or filter > them out) using the SQL database table `data` column 'flags', e.g.: > >> saulius at koala ~/ $ mysql -u cod_reader -h sql.crystallography.net cod -e 'select count(*) from data where flags not like "%has coordinates%"' >> +----------+ >> | count(*) | >> +----------+ >> | 1375 | >> +----------+ > or by analysing _atom_site_fract_x, ..._y and ..._z data items (they > contain special CIF values '?'). > > In due time, we hope to get all original publications for these > structures and deposit the coordinates, but this is done on the best > effort basis. You can help to improve COD if you have access to (some) > of these publications and can send us the atomic coordinates, preferably > in CIF format. > > Sincerely yours, > Saulius > -- Dr. Luis Ortega San Martin Dpto. Ciencias, Secci?n Quimica Pontificia Universidad Cat?lica del Peru Av. Universitaria, 1801. San Miguel Lima 32. Peru Tlf: +511 626 2000 ext.4227 alternative e-mail: luis.ortegasm at gmail.com http://www.pucp.edu.pe/profesor/luis-ortega-san-martin/ From grazulis at ibt.lt Tue Dec 5 15:19:31 2017 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Tue, 5 Dec 2017 15:19:31 +0200 Subject: [Cod-bugs] Errors with files 6000694 and 6000695 In-Reply-To: References: <3e48a001-23b7-6e97-2243-00b37755cee5@pucp.edu.pe> <0927188a-9816-f616-b469-12e7c27b872c@ibt.lt> Message-ID: <666b7f34-adc4-bb4c-02d2-820bd8edb750@ibt.lt> On 2017-12-05 15:13, Luis Ortega San Martin wrote: > Thanks for the rapid response and recommendations. > > If I can get the structure of these two compounds I will send you the > full CIF. Thanks for the suggestion, that would be great! I would then merge the new data into a new revision of the COD records. Regards, Saulius -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353 mobile: (+370-684)-49802, (+370-614)-36366