[Cod-bugs] COD Data registration

Tue Sep 17 04:38:42 EEST 2024

Dear Dr. Saulius Gražulis,

The deposited CIF files (COD accession codes: 3000469–3000476) were just released into publicly accessible repositories as published data by adding publication information.

Published paper

Cryst. Growth Des. 2024, 24, 17, 7222–7234

DOI:       10.1021/acs.cgd.4c00856

Link: https://pubs.acs.org/doi/10.1021/acs.cgd.4c00856

Here are DOI of XRDa (Xtal Raw Data Archive):

3000470

DOI: 10.51093/xrd-00261

Link: https://xrda.pdbj.org/entry/261

3000472

DOI: 10.51093/xrd-00262

Link: https://xrda.pdbj.org/entry/262

3000474

DOI: 10.51093/xrd-00263

Link: https://xrda.pdbj.org/entry/263

3000476

DOI: 10.51093/xrd-00217

Link: https://xrda.pdbj.org/entry/217

Sincerely yours,

Toshiyuki Sasaki

**************************************************************

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: Friday, August 2, 2024 6:02 PM
To: Toshiyuki Sasaki <toshiyuki.sasaki at spring8.or.jp>
Cc: cod-bugs at lists.crystallography.net
Subject: Re: COD Data registration

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  <mailto:toshiyuki.sasaki at spring8.or.jp> <toshiyuki.sasaki at spring8.or.jp>
Cc: cod-bugs at lists.crystallography.net <mailto: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:  <https://doi.org/10.51093/xrd-00142> 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

-- 
This message has been scanned for viruses and 
dangerous content by  <http://www.mailscanner.info/> MailScanner, and is 
believed to be clean. 

-- 
This message has been scanned for viruses and 
dangerous content by  <http://www.mailscanner.info/> MailScanner, and is 
believed to be clean. 

-- 
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

-- 
This message has been scanned for viruses and 
dangerous content by  <http://www.mailscanner.info/> MailScanner, and is 
believed to be clean. 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20240917/3438455f/attachment-0001.htm>