[Cod-bugs] {Disarmed} Deposition of our prepublication XRD data to COD

[Saulius Gražulis]

Dear Milad,

thank you for your interest in COD. Yes, I am aware about Iranian 
situation; I am greatly dismayed to hear that Iran blocks the Internet 
access and cracks down upon citizens.

I regret to tell you the the files that you have sent us are not 
suitable for the COD database (and this is the reason why they failed 
the validation).

COD accepts only structures with atomic coordinates in CIF format [1,2]. 
As I understood from the files that you have sent us, you conducted a 
powder diffraction experiment. To get atomic coordinates from such data, 
phasing, modelling and Rietveld refinement of the structure should be 
done. Guidelines of the IUCr procedures should be followed [3]. COD does 
not accept plain powder diffraction traces for deposition.

To deposit just a powder diffraction trace in a public repository you 
may consider uploading your files to Zenodo or Data Dryad. But even then 
you need to add a great deal of metadata to you diffraction data. As a 
bare minimum, you need to specify what was your sample and how it was 
obtained; the model and type of you measurement instrument; instrument 
settings (wavelength, X-ray tube voltage and current, slit settings, 
detector type, monochromator type, etc.); specify when, where and by 
whom the data were collected. For administrative purposes, you may want 
to specify the institution address where the measurement was performed 
and the funding source. Needless to say, data must be in some 
standardised format (e.g. CIF); original files from the instrument 
should also be provided. Plain Matlab files are not the best way to 
distribute you measurements.

Hope this helps...

Sincerely,
Saulius

Refs.:

[1] Hall, S. R.; Allen, F. H. & Brown, I. D.The crystallographic 
information file (CIF): a new standard archive file for 
crystallography/Acta Crystallographica Section A,/*1991*/, 47/, 655-685, 
DOI: https://doi.org/10.1107/S010876739101067X

[2] IUCr. Crystallographic Information Framework *2022*, URL: 
https://www.iucr.org/resources/cif; accessed 2022-11-15T14:28+02:00.

[3] David, W. I. F.; Shankland, K.; McCusker, L. B. & Baerlocher, C. 
Structure Determination from Powder Diffraction Data Oxford University 
Press, 2002, URL: https://isbnsearch.org/isbn/0199205531 .

On 2022-11-07 19:06, Milad Rasouli wrote:
>
> Dear Sir or Madam,
>
>
> I hope you are well!
>
>
> I am writing to you regarding the deposition of our prepublication 
> data to COD.
>
>
> I am trying to add our XRD data to the Crystallography Open Database, 
> but I get an error when I try to validate the data.
>
> Please find enclosed the proposed file for deposition in the 
> Crystallography Open Database.
>
>
> As you may know, Iran's government blocked internet access as the 
> protests grew. Therefore, we have limited access to the internet.
>
>
> Could you please let me know what I should do?
>
>
> This step should be completed as part of the process of publishing our 
> article in Scientific Reports. Therefore, your kind response at your 
> earliest convenience will be greatly appreciated!
>
>
> All the best,
> Milad Rasouli
>
>
>
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-- 
Dr. Saulius Gražulis
Vilnius University, Life Science Center, Institute of Biotechnology
Saulėtekio al. 7, LT-10257 Vilnius, Lietuva (Lithuania)
phone (office): (+370-5)-2234353, mobile: (+370-684)-49802, (+370-614)-36366

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