[Cod-bugs] Problems with COD

[Saulius Gražulis]

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 
> <https://www.crystallography.net/cod/check_user.php?signup>)
>
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 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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