[Cod-bugs] We cannot connect to COD

Mon Dec 29 16:56:19 EET 2025

Dear Prof. Ohnishi,

my biggest apologies that it takes so long to deposit your structures 
this time.

On a good side, I am happy to report that we have restored all 
crystallographic data on the COD server and we start accepting 
depositions in a short while.

To speed the things up for you, I will deposit the file that you have 
sent to me on 2025-12-25 as a pre-publication entry with 6 months 
embargo period on your behalf. To do this, and also to check if the COD 
deposition system is restored correctly, I'll have to reset your COD 
account’s password, and the COD system might sent you an e-mail with the 
information about the new account creation. This is a regular procedure, 
and after the deposition I'll send you instructions how to access your 
COD account, how to change the password, and how to control your 
depositions.

Sincerely yours,
Saulius

On 2025-12-25 06:47, ohnishi.yusuke.corefc at osaka-u.ac.jp wrote:
> Dear Dr. Saulius,
>
> this is Ohnishi, who previously inquired about the deposition.
> If it still looks like it will take some time to restore the COD, 
> could you please manually perform the deposition for the attached files?
> 1 CIF file and 1 corresponding FCF file are included.
> Please let me know if any information is missing.
>
> I apologize for the inconvenience, but I would appreciate your assistance.
>
> All the best,
> Ohnishi
>
> 大西　裕介 (Ohnishi Yusuke)
>
> The University of Osaka
> Core Facility Center
> Specially Appointed Assistant Professor
> I-405, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
> Tel: 06-6879-4815
> Email: ohnishi.yusuke.corefc at osaka-u.ac.jp 
> <mailto:ohnishi.yusuke.corefc at osaka-u.ac.jp>
>
>
>
> ------------------------------------------------------------------------
> *差出人:* 大西　裕介 <ohnishi.yusuke.corefc at osaka-u.ac.jp>
> *送信日時:* 2025年12月17日 9:40
> *宛先:* Saulius Gražulis <grazulis at ibt.lt>; 
> cod-bugs at lists.crystallography.net <cod-bugs at lists.crystallography.net>
> *件名:* Re: [Cod-bugs] We cannot connect to COD
> Dear Dr. Saulius
>
> thank you for your reply.
> I apologize for taking up your time while you're busy with the recovery.
> I will upload the data after the recovery is complete.
>
> Best regards,
> Ohnishi
>
> 大西　裕介 (Ohnishi Yusuke)
>
> The University of Osaka
> Core Facility Center
> Specially Appointed Assistant Professor
> I-405, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
> Tel: 06-6879-4815
> Email: ohnishi.yusuke.corefc at osaka-u.ac.jp 
> <mailto:ohnishi.yusuke.corefc at osaka-u.ac.jp>
>
> ------------------------------------------------------------------------
> *差出人:* Saulius Gražulis <grazulis at ibt.lt>
> *送信日時:* 2025年12月16日 16:23
> *宛先:* 大西　裕介 <ohnishi.yusuke.corefc at osaka-u.ac.jp>; 
> cod-bugs at lists.crystallography.net <cod-bugs at lists.crystallography.net>
> *件名:* Re: [Cod-bugs] We cannot connect to COD
> Dear Ohnishi,
>
> thank you for your e-mail. You are right, we experienced a server 
> overload and a subsequent disk crash related to a large number of 
> simultaneous bot requests. We are now busy restoring the COD server 
> and loading data from backups, which, unfortunately, might take a 
> couple of days.
>
> If the deposition is urgent please sent you files to us via e-mail and 
> I will handle them manually.
>
> I apologise for this inconvenience.
>
> Sincerely yours,
> Saulius
>
>
> On 2025-12-16 02:49, ohnishi.yusuke.corefc at osaka-u.ac.jp 
> <mailto:ohnishi.yusuke.corefc at osaka-u.ac.jp> wrote:
>> Dear COD support,
>>
>> I am Yusuke Ohnishi at the University of Osaka, Japan.
>>
>> I haven't been able to connect to the COD website since last Friday.
>> Is there some kind of trouble going on?
>>
>> I have a file I would like to deposit to COD.
>> If it takes a while to resolve, I'd like to deposit it via email if 
>> possible.
>>
>> I apologize for the trouble, but I appreciate your help.
>>
>> Best regards,
>> Ohnishi
>>
>>
>> 大西　裕介 (Ohnishi Yusuke)
>>
>> The University of Osaka
>> Core Facility Center
>> Specially Appointed Assistant Professor
>> I-405, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
>> Tel: 06-6879-4815
>> Email: ohnishi.yusuke.corefc at osaka-u.ac.jp 
>> <mailto:ohnishi.yusuke.corefc at osaka-u.ac.jp>
>>
>>
>>
>> -- 
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>>
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>
>
> -- 
> Dr. Saulius Gražulis
> Vilnius University Institute of Biotechnology, Saulėtekio al. 7
> LT-10257 Vilnius, Lietuva (Lithuania)
> mobile: (+370-684)-49802, (+370-614)-36366
>
> -- 
> This message has been scanned for viruses and
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> believed to be clean.
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> -- 
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-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366

-- 
This message has been scanned for viruses and
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