From grazulis at ibt.lt Wed Jun 25 11:19:51 2025 From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=C5=BEulis?=) Date: Wed, 25 Jun 2025 11:19:51 +0300 Subject: [Cod-bugs] Problems with COD In-Reply-To: References: <99f5c9a8ef94489ca9e0a8eafc3e7d78@tu-clausthal.de> <5f4dc75f-8d0d-4201-8c70-86022dfea4bd@ibt.lt> Message-ID: <881b1800-0d22-4579-9e52-18e534e33718@ibt.lt> Dear Peter, thank you for your request. On 2025-06-20 12:49, Peter Zugenmaier wrote: > > thank you very much for an excellent representation of introducing > personal data into COD-CIF files. I also need to intoduce a complete > CIF file into COD with the same COD number especially when > many?additional data are?added to the new file. Can you help me? > First of all, let me tell you a bit about the COD Persistent Identifiers (PID) and the COD entry policy. Each COD entry describes a single instance of a crystal structure solution and modelling. Once published, a COD ID (PID) is assigned permanently and uniquely to this structure model. We should never commit a different structure solution instance (e.g. a re-refinement) of the structure under the same ID, and should never remove the ID from the database (even if we withdraw or retract the structure). Thus, complete replacements of the old CIFs in the COD are? very rare; in fact, during the last 22 years, this hardly ever happened :). Adding additional information that was not present in the original entry is OK, as it is OK to correct small mistakes. As a rule, this does not need a complete replacement of the CIF contents ? it is safer to just append the additional information (the new CIF tags) or correct the wrong data values using a text editor. If you however still need to completely replace the content of your deposited CIF record, you can proceed as follows (actually, these are he same steps as you would do for small corrections or additions as well): - log in into the data management Web page of the COD (https://www.crystallography.net/cod/manage_depositions.php); - follow the "View your depositions " link (could take a while if you have a lot of structures deposited); - navigate to the structure you would like to replace. The structure has to be released already. Click on the structure to get the structure "card" page; - Click on the "Update" link; - After the validator has finished, click on the "Edit" button; - Scroll down to get into the editor window; - In the editor window, edit the CIF contents. If you need to replace it entirely, you can mark the whole text, delete it and/or paste a new CIF content over it. - Add a human-readable description of your update; - Click the "Save and check" button; - Check the results: -- If the structure is OK after the validator checks, click on the "Update" button. A new revision of your entry will be registered immediately. -- If there are problems detected, go back to the editor, fix them, and "Save and check" again; In case you get stuck and can not get past the validator, write me and e-mail and attach the updating CIF, with the indication of what entry it should replace (please provide the COD ID), and I'll do this manually for you. Alternatively, I can give you access to the "COD CIF staging repository", a Subversion repository where you and other COD contributors can edit a CIF collectively, and after we get the CIF right we'll transfer it to the COD. Hope this helps. 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: