[Cod-bugs] COD Data registration

Thu Aug 8 15:23:08 EEST 2024

Dear Dr. Saulius Gražulis

Sorry for the lack of information.

Deposited data and related information

3000560:

taca-ina-meno2_fill.cif

data_taca-ina-meno2

merged 13 crystals

Removed lines for the deposition

_refine_ls_wR_factor_ref         0.4090

3000561:

TACA-INA-Toluene_fill.cif

data_taca-ina-toluene

merged 9 crystals

Removed lines for the deposition

_refine_ls_R_factor_gt           0.1540

_refine_ls_wR_factor_ref         0.3972

> BTW, will your your colleagues be at the ECM34? It would be nice to meet
and talk in person :)
I will not be there and I don't know whether my collaborators join the
ECM34 or not.
Anyway, I mentioned about you and if someone will attend the ECM34, he will
contact you :)

Best regards,

Toshiyuki Sasaki

2024年8月2日(金) 18:02 Saulius Gražulis <grazulis at ibt.lt>:

> 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 <grazulis at ibt.lt>]
> *Sent:* Thursday, June 27, 2024 3:18 PM
> *To:* Toshiyuki Sasaki <toshiyuki.sasaki at spring8.or.jp>
> <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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