From elifantbursali at gmail.com Thu Feb 22 13:20:29 2024 From: elifantbursali at gmail.com (=?UTF-8?Q?EL=C4=B0F_ANT_BURSALI?=) Date: Thu, 22 Feb 2024 14:20:29 +0300 Subject: [Cod-bugs] COD and JCPDS card number Message-ID: Dear official, I need to obtain the COD number or JCPDS card number by using the raw XRD data of a new synthesized substance. Are these two numbers the same? How can I access these numbers? Can you help me if I send you the raw XRD data of my material? I am in a very difficult situation. In order for the article to be published, I need to index the complex with the JCPDS card number. I have quite limited time. I'm sorry for taking up your valuable time. I'm looking forward to your response. Yours sincerely. Dr. Elif Ant Bursal? Dokuz Eylul University Faculty of Sciences Department of Chemistry -- 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 grazulis at ibt.lt Thu Feb 22 17:16:26 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Thu, 22 Feb 2024 17:16:26 +0200 Subject: [Cod-bugs] COD and JCPDS card number In-Reply-To: References: Message-ID: Dear Elif, On 2024-02-22 13:20, EL?F ANT BURSALI wrote: > > I need to obtain the COD number or JCPDS card number by using the raw > XRD data of a new synthesized substance. Are these two numbers the same? > No, they are not. COD and JCPDS (probably you mean PDF, teh Powder Diffraction File) are different databases, not related to each other (in fact, the PDF is commercial and closed, so we do not even have access to it). Correspondingly the identifiers of the two databases are different, they are in different name spaces so to speak. > > How can I access these? numbers? Can you help me if I send you the raw > XRD data of?my?material? > Unfortunately, not. We do not offer a service to process or handle raw diffraction data for researchers, at least not at the moment. > > I am in a very difficult situation. In order for the article to be > published, I?need to index the complex with the JCPDS card number. I > have quite limited time. I'm sorry for taking up your valuable time. > I'm looking forward to your response. Yours sincerely. > We do not accept raw powder diffraction traces to the COD. For the data to be suitable for COD, one needs to solve the atomic resolution structure, refine it (e.g. using the Rietveld method) and the submit to the COD both the atomic coordinates of the model and the original diffractograms. The raw powder diffraction data can probably be deposited to the PDF of the ICDD (https://www.icdd.com/), but you need to contact them to find out what their requirements would be. Alternatively, you can upload data to a generic repository like Zenodo (https://zenodo.org/) and get a DOI for it, but the data will not undergo any peer review there and will be harder to find (although it will be open). Sincerely yours, Saulius -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- 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 grazulis at ibt.lt Thu Feb 22 17:45:18 2024 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Thu, 22 Feb 2024 17:45:18 +0200 Subject: [Cod-bugs] COD database In-Reply-To: <1708291648.371496604@f752.i.mail.ru> References: <1708291648.371496604@f752.i.mail.ru> Message-ID: Dear Hasmik, On 2024-02-18 23:27, Hasmik Kirakosyan wrote: > I am a senior researcher at the Institute of Chemical Physics after A. > B. Nalbandyan NAS RA > I am studying the preparation of various inorganic materials by > combustion synthesis. The data on the phase composition collected by a > MiniFlex 600 Rigaku Smart Lab SE diffractometer (Rigaku Corporation, > Tokyo, Japan) with a D/teX Ultra 250 1D detector and with a Cu-K? > radiation (?=0.154 nm) at 40 kV and 15 mA, then processed via the COD > database. > Can you tell if the COD database is updated automatically or not? And > can this program be updated from time to time? I am not quite sure what your question is. The COD is an open crystal structure database [1,2]; it hosts crystal structures solved by diffraction methods in CIF [3] format. As such, the COD can not "process" a file; it just provides data about crystal structures. Different vendors, Rigaku among them, compile the COD into their own databases that are used for search-match material identification, and possibly other uses (e.g. initial approximations for the Rietveld refinement), and ship those derived databases along with their hardware and software. If you are using Rigaku software to process your data or to identify materials, chances are that you are using COD data in the Rigaku database [4] in their software packages. We, the COD developers, although we collaborate with diffractometer vendors on data management and sometimes even host their derived databases, do not compile data for any companies' software and do not influence updates. The companies themselves decide when and how to update their search-match databases from the new COD revisions. As I see now, Rigaku has quite an old release, from 2020. If you have still older release, you can download the 2020 database from the COD site [4], but please check if it is compatible with your software. If you already have the 2020 release and you can not find the material you need there, I suggest writing an e-mail to Rigaku directly and ask them if they can ship you an updated version. They can and may download the data from the COD at any time, our license is CC0 :). Hope this helps, Saulius Refs.: [1] Gra?ulis, S.; Chateigner, D.; Downs, R. T.; Yokochi, A. F. T.; Quir?s, M.; Lutterotti, L.; Manakova, E.; Butkus, J.; Moeck, P. & Le Bail, A. (2009) Crystallography Open Database -- an open-access collection of crystal structures. Journal of Applied Crystallography 42, 726-729. DOI: https://doi.org/10.1107/S0021889809016690. [2] Gra?ulis, S.; Da?kevi?, A.; Merkys, A.; Chateigner, D.; Lutterotti, L.; Quir?s, M.; Serebryanaya, N. R.; Moeck, P.; Downs, R. T. & Le Bail, A. (2012) Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration. Nucleic Acids Research 40, D420-D427. DOI: https://doi.org/10.1093/nar/gkr900. [3] Hall, S. R.; Allen, F. H. & Brown, I. D. (1991) The crystallographic information file (CIF): a new standard archive file for crystallography. Acta Crystallographica Section A 47, 655-685. DOI: https://doi.org/10.1107/S010876739101067X. [4] Rigaku (2020) COD for Rigaku softwares. URL: http://www.crystallography.net/cod/archives/2020/Rigaku/ [accessed 2024-02-22T17:39+02:00]. -- Dr. Saulius Gra?ulis Vilnius University Institute of Biotechnology, Saul?tekio al. 7 LT-10257 Vilnius, Lietuva (Lithuania) mobile: (+370-684)-49802, (+370-614)-36366 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.