From az.processor at gmail.com Fri Nov 24 19:10:34 2023 From: az.processor at gmail.com (aref zarei) Date: Fri, 24 Nov 2023 20:40:34 +0330 Subject: [Cod-bugs] getting help for COD database file parsing Message-ID: Hi there. I am a researcher in the area of signal analysis. I'm a Msc student of Biomedical Engineering at MUI. I wanted to do some experiments in composition match finding in the COD database. I was wondering if you would mind helping me in parsing the data of COD23_HS4x.hsrdb. In this database file, is there data of the pattern of each chemical composition in the form of 2? and intensity ? If not, where can I find this type of data? can it be generated from some other data present in the database file? thanks in advance. sincerely yours: Aref -- 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 kkitahara5101 at gmail.com Sat Nov 25 03:28:51 2023 From: kkitahara5101 at gmail.com (Koichi Kitahara) Date: Sat, 25 Nov 2023 10:28:51 +0900 Subject: [Cod-bugs] Some structures published in Acta Cryst. E are missing in COD Message-ID: To whom it may concern, I found that some structures published in Acta Cryst. E are missing in COD. Are there any criteria for structures to be available in COD, or are there some bugs in automatic extraction routines of COD? In particular, I'm wondering if our structures [1] will be available in COD in near future or not. [1] https://doi.org/10.1107/S2056989023008393 Best regards, Koichi Kitahara -- 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 amelia.sparavigna at polito.it Sat Nov 25 12:45:52 2023 From: amelia.sparavigna at polito.it (Amelia Sparavigna) Date: Sat, 25 Nov 2023 10:45:52 +0000 Subject: [Cod-bugs] Problems with SOLSA Database Message-ID: Dears, first, let me congratulate for your precious database. This summer I have used some Raman spectra from SOLSA. But, today, it is impossible to reach the data at the following address: https://solsa.crystallograohy.net/rod/ for instance, https://solsa.crystallography.net/rod/3500283.rod I wrote to Dr. El Mendili, but the mail system told me the address was wrong. Please, could you check the SOLSA status and tell me how I can reach again the Raman data (may be through alternative search oages). Thank you again, Amelia Sparavigna Politecnico di Torino -- 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 Sat Nov 25 12:49:12 2023 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sat, 25 Nov 2023 12:49:12 +0200 Subject: [Cod-bugs] Problems with SOLSA Database In-Reply-To: References: Message-ID: <1cfce6da-bfc0-d096-9724-264c3370031c@ibt.lt> Hi, Amelia, thanks for reaching us. The address that you chose for reporting problems is the right one. There is indeed a problem with the SOLSA server, we'll investigate and get back to you when it is fixed. Sincerely yours, Saulius On 2023-11-25 12:45, Amelia Sparavigna wrote: > Dears, > > first, let me congratulate for your precious database. > > This summer? I have used some Raman spectra from SOLSA. > But, today, it is impossible to reach the data at the following address: > https://solsa.crystallograohy.net/rod/ > > for instance, > https://solsa.crystallography.net/rod/3500283.rod > > I wrote to? Dr. El Mendili, but the mail system told me the address > was wrong. > > Please, could you check the SOLSA status and tell me how I can reach > again the Raman data (may be through alternative search oages). > > Thank you again, > > Amelia Sparavigna > Politecnico di Torino > > -- > 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 -- 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 -- 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 -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/vcard Size: 4 bytes Desc: not available URL: From grazulis at ibt.lt Sat Nov 25 13:19:47 2023 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=) Date: Sat, 25 Nov 2023 13:19:47 +0200 Subject: [Cod-bugs] Problems with SOLSA Database In-Reply-To: References: Message-ID: <4c4b20e1-c0be-04af-3783-d9be33ed427f@ibt.lt> Dear Amelia, I have restarted the ROD server and it is now operational. It seems that it was overwhelmed by bots (we'll think how to deal with this, such stalls happen from time to time). Please let us know if the database works or if there are any other problems. Sincerely yours, Saulius On 2023-11-25 12:45, Amelia Sparavigna wrote: > This summer? I have used some Raman spectra from SOLSA. > But, today, it is impossible to reach the data at the following address: > https://solsa.crystallograohy.net/rod/ > > for instance, > https://solsa.crystallography.net/rod/3500283.rod > > I wrote to? Dr. El Mendili, but the mail system told me the address > was wrong. > > Please, could you check the SOLSA status and tell me how I can reach > again the Raman data (may be through alternative search oages). > -- 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 -- 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 -------------- A non-text attachment was scrubbed... Name: grazulis.vcf Type: text/vcard Size: 4 bytes Desc: not available URL: From gunnej at chemie.uni-siegen.de Sat Nov 25 14:33:29 2023 From: gunnej at chemie.uni-siegen.de (=?iso-8859-1?Q?Schmedt_auf_der_G=FCnne=2C_J=F6rn=2C_Prof=2E_Dr=2E?=) Date: Sat, 25 Nov 2023 12:33:29 +0000 Subject: [Cod-bugs] incomplete entries Message-ID: Dear COD team, thank you very much for putting up such a nice database. I am relying on it because our university cannot afford to pay the money for the CSD. I appreciate a lot the sql-interface. The reason why am writing is I have several questions. 1.) I am/was writing some tcl-tk-scripts to search for compounds and a useful strategy which I used in other databases was to suppress all unwanted elements to produce all possible structures in a composition space which could be compared with experimental data. For the COD I stumbled over a problem. Such a search produces a lot of structures where the composition formula is missing. I also fond a number of entries with missing fractional coordinates or where only a unit cell was specified but no structure was provided (elements markes as "?"). Is it intended to have such structures in the database or are such structures "unwanted"? I saw that upon submission there is a quality check which I think should stop such structures from deposition in the database. 2.) How can I mark a structure as disordered upon submission? 3.) How can I help to revise errors of structures which I find in the database which have not been submitted by me? I am sorry if I should have overlooked answers in the COD wiki, but I didn't find the information there. Best regards, J?rn Schmedt auf der G?nne https://www.chemie-biologie.uni-siegen.de/ac/jsadg -- 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: