[Cod-bugs] Deposition to the COD [Was: Re: hi]

[Saulius Gražulis]

Dear Fatemeh,

On 2023-03-13 12:33, Fatemeh Oshani wrote:
> Thanks for your guidance. I want to deposit my data for COD and 
> provide the number ID for submission to the journal. I don't know how 
> to write Cif data.

In order to deposit the data to the COD, a structure with new 
coordinates must be solved. From your e-mail I have impression that you 
use powder diffraction to characterise your samples. In that case, using 
e.g. Le Bail method [1] and/or Rietveld refinement [2] can yield atomic 
coordinates of your material. Programs like GSAS [3,4] can help with 
this and they write out CIFs of appropriate structure. The IUCr has 
several textbooks on powder diffractometry [5,6].

> The COD ID of the peaks in the sample was found, and the CIF of the 
> identified material was deposited, but it was incorrect.
> I need assistance with depositing data into COD.

Just identifying a material is not enough to deposit data to the COD; 
you need to solve a new structure for the data to be eligible for COD.

If you have just run a diffractogram recording an identified material, 
and this materail contains know structures from the COD, you can not 
deposit these data to COD. If you need and ID for your publication, I 
suggest using Zenodo (https://zenodo.org/), Data Dryad 
(https://datadryad.org/stash) of FigShare (https://figshare.com/) to 
deposit your data files.

Hope this helps, Saulius

Refs.:

[1] https://en.wikipedia.org/wiki/Le_Bail_method [accessed 
2023-03-14T10:10+02:00]

[2] https://en.wikipedia.org/wiki/Rietveld_refinement [accessed 
2023-03-14T10:11+02:00]

[3] https://www.ncnr.nist.gov/xtal/software/gsas.html [accessed 
2023-03-14T10:14+02:00]

[4] https://subversion.xray.aps.anl.gov/trac/pyGSAS [accessed 
2023-03-14T10:13+02:00]

[5] Young, R. A. The Rietveld Method. IUCr; Oxford University Press, 
1995, ISBN: 0198559127, URL: https://www.worldcat.org/search?q=bn:0198559127

[6] David, W. I. F.; Shankland, K.; McCusker, L. B. & Baerlocher, C. 
Structure Determination from Powder Diffraction Data. Oxford University 
Press, 2002, ISBN: 0198500912, URL: 
https://www.worldcat.org/search?q=bn:0198500912

-- 
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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