[Cod-bugs] COD Data registration

[Saulius Gražulis]

Dear Dr. Toshiyuki,

thank you for the e-mail! I'll insert the ...R_factor_... data names 
into you submitted CIFs where necessary.

Regarding the references to the image locations, there are two 
mechanisms that that we consider using. One is the IUCr suggestion by 
Brian McMahon announced at the IUCr Congress last year. Another is the 
intrinsic COD mechanism using the '_cod_related_entry_[]' category. Both 
requite certain update of the COD infrastructure, which I plan to do, 
hopefully, before leaving to the ECM34 this month.

The '_cod_related_entry_[]' at the moment looks like this:

> saulius at tasmanijos-velnias cod-tools/ $ tail -5 
> /home/saulius/struct/cod/current/cif/9/01/51/9015157.cif
> loop_
> _cod_related_entry_id
> _cod_related_entry_database
> _cod_related_entry_code
> 1 AMCSD 0018609
In a similar way, we could use an external database, say XRDA [1], and 
gibe a link to the database's record (unique ID).

For this I need to make an additional SQL table in the COD, xrda_x_cod, 
and update the COD deposition scripts so that they populate that new 
table. It is not a large work, I just need to find two free days to 
implement and test this :)

BTW, will your your colleagues be at the ECM34? It would be nice to meet 
and talk in person :)

Regards,
Saulius

On 2024-08-02 08:04, Toshiyuki Sasaki wrote:
>
> Dear Dr. Saulius Gražulis,
>
> I have uploaded crystal structures with some errors solved by MicroED 
> to COD.
>
> By following the previous procedures (remove lines and give you 
> information about the errors etc.), I would like you to handle the 
> data properly.
>
> Deposited data and related information
>
> 3000560: merged 13 crystals
>
> Removed lines for the deposition
>
> _refine_ls_wR_factor_ref         0.4090
>
> 3000561: merged 9 crystals
>
> Removed lines for the deposition
>
> _refine_ls_R_factor_gt           0.1540
>
> _refine_ls_wR_factor_ref         0.3972
>
> Regarding EM images, what can I do?
>
> “I'll come back to your shortly with a suggested update of your data 
> files.“
>
> Thank you for your cooperation.
>
> Best regards,
>
> Toshiyuki
>
> **************************************************************
>
> 公益財団法人高輝度光科学研究センター
>
> (Japan Synchrotron Radiation Research Institute(JASRI))
>
> 回折・散乱推進室(Diffraction and Scattering Division)
>
> テニュアトラック研究員(Tenure-track researcher)
>
> 佐々木　俊之(Dr. Toshiyuki Sasaki)
>
> TEL: 0791-58-0802(3430)
>
> 〒679-5198　兵庫県佐用郡佐用町光都1丁目1番1号
>
> (1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 Japan)
>
> **************************************************************
>
> *From:*Saulius Gražulis [mailto:grazulis at ibt.lt]
> *Sent:* Thursday, June 27, 2024 3:18 PM
> *To:* Toshiyuki Sasaki <toshiyuki.sasaki at spring8.or.jp>
> *Cc:* cod-bugs at lists.crystallography.net
> *Subject:* Re: COD Data registration
>
> On 2024-06-27 09:14, Toshiyuki Sasaki wrote:
>
>     Finally our paper was published on Journal of Materials Chemistry C.
>
>     The deposited CIF files (3000450, 3000451) were just updated by
>     including publication information.
>
>     In addition, I give you DOI of XRDa of these structures as I promised.
>
>     3000450, 3000451: 10.51093/xrd-00142
>     <https://doi.org/10.51093/xrd-00142>
>
> Thanks a lot for your update, and congratulations with your publication!
>
> I'll have a look at the data. Also, I remember that your have 
> published the links to original EM images; it would be great to 
> include these links into the COD files as well. We have recently 
> developed a mechanism how this can be done,; I'll come back to your 
> shortly with a suggested update of your data files.
>
> 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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-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
mobile: (+370-684)-49802, (+370-614)-36366

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