From peter.zugenmaier at tu-clausthal.de Mon Jun 16 00:30:19 2025 From: peter.zugenmaier at tu-clausthal.de (Peter Zugenmaier) Date: Sun, 15 Jun 2025 21:30:19 +0000 Subject: [Cod-bugs] Problems with COD Message-ID: Sirs, I have problems with loading sligtly changed CIF-Files to COD, which were deposited as ?prepublication data? during review. Depositing the changed files by "already published structure" does not work. Enclosed find a letter-pdf file, which I hope explains my problem. Are you able to help me? Kind regards, Peter Zugenmaier Professor of Physical Chemistry TU Clausthal, Germany -- 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: Letter.pdf Type: application/pdf Size: 276677 bytes Desc: Letter.pdf URL: From grazulis at ibt.lt Tue Jun 17 12:09:29 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Tue, 17 Jun 2025 12:09:29 +0300 Subject: [Cod-bugs] Problems with COD In-Reply-To: References: Message-ID: Dear Prof. Zugenmaier, thank you for your inquiry. Sure we can resolve the issue! On 2025-06-16 00:30, Peter Zugenmaier wrote: > > I have problems with loading sligtly changed CIF-Files to COD, which > were deposited as ?prepublication data? during review. Depositing the > changed files by?"already published structure" does not work. > > Enclosed find a letter-pdf file, which I hope explains my problem. > > Are you able to help me? > Indeed, depositing the same structure with slightly changed metadata would result in a duplicated structure and is therefore prevented by the COD deposition software. We should update the previously deposited structure and issue a new revision for it. One of the ways you can do that yourself is to login in into the COD deposition management page (following the "Manage depositions" link on the COD home page, or following the link below): https://www.crystallography.net/cod/manage_depositions.php Then click on the "View your depositions " link. You should get the list of the COD entries deposited by you. You can then click on a particular structure, get the structure page; you should then get an "update" link on that page and if you navigate to that link, you should be able to click "edit" after the entry is checked, and deposit a new revision of that entry. Entries that are "on hold" can be released using the "Manage/release your prepublications " link. ---- If this does not work however we can update the files for you. Let me restate how I understand the current situation: - you wold like to release your structures with the COD IDs 3000482, 3000483, 3000484 (for the first paper) and 3000576, 3000577 (for the second paper) to the public; - you would like to full bibliographic data to your entries: for COD entries 3000573?3000583: Zugenmaier, P. (2025). Comparison of Selected Crystal Structures of Rod-like Molecules with Acid and Ester Terminal Groups. /Crystals/, /15/(2), 102. https://doi.org/10.3390/cryst15020102 for COD entries COD 3000482, 3000483, 3000484: Zugenmaier, P. (2024). Crystal and Molecular Structures of Two Phthalocyanines, Chloro(phthalocyaninato)gallium(III) (ClGaPc) and ?-Oxobis(phthalocyaninato)gallium(III) (PcGaOGaPc). /Crystals/, /14/(2), 182. https://doi.org/10.3390/cryst14020182 If you confirm that the this is your intention and the above information is correct then I'll release the COD entries 3000573?3000583 and 3000482?3000484 into the public. 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 zhangy3 at ornl.gov Tue Jun 17 20:38:38 2025 From: zhangy3 at ornl.gov (Zhang, Yuanpeng) Date: Tue, 17 Jun 2025 17:38:38 +0000 Subject: [Cod-bugs] API issue Message-ID: Dear COD team, I am writing to report a bug with the following API calls, http://www.crystallography.net/cod/result.php?el1=C&el2=Ca&el3=O&strictmax=3&format=lst I think it is supposed to be returning a text file with a list of IDs of the resulted structures. However, now the returned text file is something like attached. It will be very nice if you can help debug this feature. Really appreciate it and thank you! Cheers, Yuanpeng -- Dr. Yuanpeng Zhang Neutron Scattering Scientist Spallation Neutron Source Oak Ridge National Laboratory 1 bethel valley road, Oak Ridge, TN 37830, US Mobile: +1(865)-335-4818 Email: zhangy3 at ornl.gov | Web: https://me.iris-home.net -- 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 -------------- An embedded and charset-unspecified text was scrubbed... Name: COD-numbers.txt URL: From grazulis at ibt.lt Wed Jun 18 07:27:31 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Wed, 18 Jun 2025 07:27:31 +0300 Subject: [Cod-bugs] API issue In-Reply-To: References: Message-ID: <378f4171-0b35-40c3-87af-dc4303ac0eed@ibt.lt> On 2025-06-17 20:38, Zhang, Yuanpeng wrote: > > I am writing to report a bug with the following API calls, > > http://www.crystallography.net/cod/result.php?el1=C&el2=Ca&el3=O&strictmax=3&format=lst > > > I think it is supposed to be returning a text file with a list of IDs > of the resulted structures. However, now the returned text file is > something like attached. > > It will be very nice if you can help debug this feature. Really > appreciate it and thank you! > Thanks for the report, this is definitely a bug, we'll fix it ASAP. -- 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 andrius.merkys at gmail.com Wed Jun 18 13:15:26 2025 From: andrius.merkys at gmail.com (Andrius Merkys) Date: Wed, 18 Jun 2025 13:15:26 +0300 Subject: [Cod-bugs] API issue In-Reply-To: References: Message-ID: Hi Yuanpeng, On 2025-06-17 20:38, Zhang, Yuanpeng wrote: > I am writing to report a bug with the following API calls, > > http://www.crystallography.net/cod/result.php?el1=C&el2=Ca&el3=O&strictmax=3&format=lst > > I think it is supposed to be returning a text file with a list of IDs of > the resulted structures. However, now the returned text file is > something like attached. > > It will be very nice if you can help debug this feature. Really > appreciate it and thank you! Thank you for reporting this issue. Indeed, there was an API bug on our side. We have fixed it, you should be able to repeat your query and get the list of IDs, as expected. Best wishes, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, 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. From zhangy3 at ornl.gov Wed Jun 18 16:38:00 2025 From: zhangy3 at ornl.gov (Zhang, Yuanpeng) Date: Wed, 18 Jun 2025 13:38:00 +0000 Subject: [Cod-bugs] [EXTERNAL] Re: API issue In-Reply-To: References: Message-ID: Thank you so much for your quick fix! Really appreciate it! Cheers, Yuanpeng -- Dr. Yuanpeng Zhang Neutron Scattering Scientist Spallation Neutron Source Oak Ridge National Laboratory 1 bethel valley road, Oak Ridge, TN 37830, US Mobile: +1(865)-335-4818 Email: zhangy3 at ornl.gov | Web: https://me.iris-home.net From: Andrius Merkys Date: Wednesday, June 18, 2025 at 06:16 To: Zhang, Yuanpeng Cc: cod-bugs at ibt.lt Subject: [EXTERNAL] Re: [Cod-bugs] API issue Hi Yuanpeng, On 2025-06-17 20:?38, Zhang, Yuanpeng wrote: > I am writing to report a bug with the following API calls, > > https:?//urldefense.?us/v2/url?u=http-3A__www.?crystallography.?net_cod_result.?php-3Fel1-3DC-26el2-3DCa-26el3-3DO-26strictmax-3D3-26format-3Dlst&d=DwIDaQ&c=v4IIwRuZAmwupIjowmMWUmLasxPEgYsgNI-O7C4ViYc&r=FFVJEhliaRWvn1o7oJgZImpxTRec6XXCpU8htYF_j4s&m=3dwvqoHS6nc-SfciOtPfnnN6twg6uoAtq--X4cx0g-FkEIGgB6U9aGIYqasq8ikN&s=ptsaoEV1gj-fMaIGTMJEhXV-lWOIeZeFYQ6v4nSGugw&e= Hi Yuanpeng, On 2025-06-17 20:38, Zhang, Yuanpeng wrote: > I am writing to report a bug with the following API calls, > > https://urldefense.us/v2/url?u=http-3A__www.crystallography.net_cod_result.php-3Fel1-3DC-26el2-3DCa-26el3-3DO-26strictmax-3D3-26format-3Dlst&d=DwIDaQ&c=v4IIwRuZAmwupIjowmMWUmLasxPEgYsgNI-O7C4ViYc&r=FFVJEhliaRWvn1o7oJgZImpxTRec6XXCpU8htYF_j4s&m=3dwvqoHS6nc-SfciOtPfnnN6twg6uoAtq--X4cx0g-FkEIGgB6U9aGIYqasq8ikN&s=ptsaoEV1gj-fMaIGTMJEhXV-lWOIeZeFYQ6v4nSGugw&e= > > I think it is supposed to be returning a text file with a list of IDs of > the resulted structures. However, now the returned text file is > something like attached. > > It will be very nice if you can help debug this feature. Really > appreciate it and thank you! Thank you for reporting this issue. Indeed, there was an API bug on our side. We have fixed it, you should be able to repeat your query and get the list of IDs, as expected. Best wishes, Andrius -- Andrius Merkys Vilnius University Institute of Biotechnology, 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 robert.mcmeeking at stfc.ac.uk Thu Jun 19 11:06:18 2025 From: robert.mcmeeking at stfc.ac.uk (Robert McMeeking - STFC UKRI) Date: Thu, 19 Jun 2025 08:06:18 +0000 Subject: [Cod-bugs] Missing Journal Information In-Reply-To: References: Message-ID: Hi Antanas & Saulius I do appreciate that getting the full bibliography details is not the major COD priority, especially when a DOI link is available. But have you had any further thoughts on the entries linked to in my previous email? I was thinking of making some more checks. Best Regards Bob Sent from Outlook for Android ________________________________ From: McMeeking, Robert (STFC,DL,SC) Sent: Wednesday, April 9, 2025 3:58:47 PM To: 'Antanas Vaitkus' Cc: 'cod-bugs at ibt.lt' ; McMeeking, Robert (STFC,DL,SC) Subject: RE: [Cod-bugs] Missing Journal Information Hello again, Antanas & Saulius I have checked the problem entries via CrossRef and it looks like the updated bibliographic information is now in place. Are there corrections in the pipeline on the COD system? Is it possible that CrystalWorks has not picked up the corrections yet? Here is a link to the set of entries with journal title information: https://cds.dl.ac.uk/cgi-bin/rfm/crystalworks_trawl_new?8799_8892_9714 Best Regards Bob From: McMeeking, Robert (STFC,DL,SC) Sent: 07 April 2025 17:04 To: 'Antanas Vaitkus' Cc: cod-bugs at ibt.lt Subject: RE: [Cod-bugs] Missing Journal Information Hello Antanas & Saulius Thanks for the quick reply. I had noticed that full bibliographic information was not always for new entries. I realise that additional information (such as page numbers) may be added using, for instance, CrossRef is often added at a later state. What had confused me was there now appear to more entries where the title of the journal is not present. The ones I have noticed are from IUCr journals. I assume this information would usually be in the CIF file. Do you know whether there has been a change in the way the publisher handles these things now? Best Regards Bob From: Antanas Vaitkus > Sent: 07 April 2025 12:20 To: McMeeking, Robert (STFC,DL,SC) > Cc: cod-bugs at ibt.lt Subject: Re: [Cod-bugs] Missing Journal Information Dear Robert, First of all, thank you for your report. Let me slightly expand on Saulius' response. Entries that are automatically deposited to the COD often lack the full bibliographic data upon the initial commit. While the DOI is usually known, other bibliographic data might be more difficult to determine automatically (e.g. services such as CrossRef may take up to a few months to update their bibliography related to a given DOI). Due to this we tend to record the DOI upon the initial commit and then come back and add the full bibliography in an automated fashion at a later date. The entry that you noticed is most likely just in the queue to be updated. It is very likely that you will stumble upon a few more entries like these, but they should be viewed more as "in progress" than as having issues. Sincerely Antanas On Mon, 7 Apr 2025 at 13:00, Robert McMeeking - STFC UKRI > wrote: Dear Antanas, et al. I have noticed a problems with the COD 1573685. This provides author information for the entry but no journal information. The DOI is available. So I assume these details can now be added. Best Regards Bob McMeeking -- 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 grazulis at ibt.lt Thu Jun 19 11:53:27 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Thu, 19 Jun 2025 11:53:27 +0300 Subject: [Cod-bugs] Missing Journal Information In-Reply-To: References: Message-ID: On 2025-06-19 11:06, Robert McMeeking - STFC UKRI wrote: > I do appreciate that getting the full bibliography details is not the > major COD priority, especially when a DOI link is available. But have > you had any further thoughts on the entries linked to in my previous > email? > > I was thinking of making some more checks. > If you could convert that information to a .patch file (diff) against the existing COD CIF, we could then apply it and commit after the check. Is that a lot of work on your side? Alternatively, can you generate the information in some machine readable form (CSV or TSV preferred)? Regards, 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 Jun 19 17:47:20 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Thu, 19 Jun 2025 17:47:20 +0300 Subject: [Cod-bugs] Problems with COD In-Reply-To: <99f5c9a8ef94489ca9e0a8eafc3e7d78@tu-clausthal.de> References: <99f5c9a8ef94489ca9e0a8eafc3e7d78@tu-clausthal.de> Message-ID: <5f4dc75f-8d0d-4201-8c70-86022dfea4bd@ibt.lt> On 2025-06-19 16:57, Peter Zugenmaier wrote: > > Dear Dr. Grazulis, > > Thank you for your fast reply. To login into the COD deposition > management occurs by: > > *Account Management Interface* > > Depositor details (sign up > ) > Dear Peter, thank you for the deposition details. Below I outlined a general procedure for releasing data which I followed from your session. I performed all steps except the last one for the structure COD 3000482, but did not press the release button so that it does not interfere with your deposition process; I would appreciate if you check these steps and, if they work, press the deposit button from your side. Here are the steps: 1. Log in into your deposition management interface at https://www.crystallography.net/cod/my_depositions.php?filter=prepublications . After you enter your name and password you should be forwarded to the Account Management Interface: screen_01.png Click on the "Manage/release your prepublications" link. 2. You should get the Prepublication Deposition list. Find the COD ID that you would like to release after the publication and cklick "Update" next to the COD ID: screen_02.png 3. In the appearing Validation and Deposition Interface please select "Release data into publicly accessible repository as published data" and click "Begin update": screen_03.png 4. After the COD server checks the structure (it may take some while) you should get the structure validation page. It will have some warnings about the missing bibliography ? that's OK at this stage. Please select the "Edit" button: screen_04.png 5. A detailed warning list will appear: screen_05.png Please scroll down to reach the editor window. 6. In the editor window, please paste the publication DOI and click "Fetch": screen_06.png (you can, of course, enter the bibliography by hand by the DOI fetcher usually does all the printing for you :) 7. You should get the "Bibliography was uploaded ..." page: screen_07.png Please scroll down to verify that the bibliography is correct. 8. If the inserted information is right, please click "Save and check" button: screen_08.png 9. The system should now return a new Validation page with a message "File ... is correct" on a green background. The notices on a blue background are just for your information and do not preclude release of the structure: screen_09.png 10. Click "update". You should be informed that the structure has been released and it should appear on the public COD Web site with the full bibliography and other metadata. Hope this helps. There might be a small caveat here since your name as the structure author contains both your first name and your surname, but your login name is just your surname. But for the published structures this should be OK. Please let me know if this procedure works for you or if some further assistance is needed. 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: screen_01.png Type: image/png Size: 142994 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: screen_02.png Type: image/png Size: 285042 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: screen_03.png Type: image/png Size: 160010 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... 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