[Cod-bugs] Problems with COD

[Saulius Gražulis]

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 
<https://www.crystallography.net/cod/my_depositions.php?CODSESSION=r3iha5puaaud9aijmfnbdi1dki>" 
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 Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366

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