[Cod-bugs] COD to PDF

[Silvina Di Pietro]

Hi Saulius,
First of all,  I truly appreciate you responding my email and answering my inquiry. You went into great detail.
You answered my question when you stated "we are explicitly forbidden to take any data from them, including their identifiers. This restrictiveness is actually one of the main reasons why the COD was started!"
I did not mean "Page Description File from Adobe'' but "Powder Diffraction File''.
The last two sentences are of great importance as I did not know there was a difference between the two (PDF and COD). I mostly work with clays (illite, muscovite and montmorillonite) so this statement "scattering data even in cases when the atomic structure of material is not known" is good to know since our XRD got the PDF ICDD database as well. I wonder how I am able to know that the atomic structure is not known if the software does the match to my minerals. I'll have to give it a try.
Again, I thank you for your time.
Have a great day,
-Silvi


________________________________
From: Saulius Gražulis
Sent: Tuesday, February 25, 2020 1:05 AM
To: Silvina Di Pietro
Cc: cod-bugs at lists.crystallography.net
Subject: Re: [Cod-bugs] COD to PDF

Dear Silvi,

thank you for your message. I'll try to answer your questions below, although I need more context for my answers to be more precise.

The short answer would be that we maintain no links with ICDD PDF entries or any other commercial databases. Commercial databases have restrictive licenses, and we are explicitly forbidden to take any data from them, including their identifiers. This restrictiveness is actually one of the main reasons why the COD was started!

On 2020-02-18 21:02, Silvina Di Pietro wrote:
I had a simple question: I am currently using Eva software on my school's XRD lab. Whenever I match, I get specific COD #. I was wondering if this # could be "translated" into PDF from the ICDD database.

What you mean by „PDF“ in this context? Do you mean a Page Description File from Adobe (PDF), generated by ICDD software for a crystallographic entry, or do you mean a record identifier from the powder Diffraction File (PDF) marketed by ICDD?

In both cases the answer would be "no", but for different reasons, and thus the workarounds would be different:

- if you want a (nice) page description file (PDF) for a structure, then of course we can not run the ICDD software for you on our servers (the software is proprietary), but you can use your browser to find a particular COD structure easily if you know its COD ID – either use the COD "Search" page and paste the COD ID into the "Search by COD ID:" field, or construct a stable URI for this structure, e.g. for the COD ID 7239975 it would be:

https://www.crystallography.net/cod/7239975.html

You can then of course use your browser's "print to file" functionality to produce a PDF file.

- if you want a corresponding Powder Diffraction File (PDF) identifier, then you have to search for the structure in the PDF using their provided software for the same material. You will have to own a license for PDF to do that (I do not know how you get it – consult you University's purchase/licensing dept. or ICDD marketing people). You can then take representative structure parameters (cell, spacegroup, atomic composition, name, publication data, etc.) from the COD (e.g. from the structure Web page, as mentioned above), and paste those values into the PDF search. The search should yield the structure or structures of the same material, if they exists in the PDF :)

Is there a way that the same COD # could exist for PDF?

Since both the COD and the PDF collect published structural data from scientific sources, they should overlap to a large extent (I do not know how much, because I do not have access to the ICSD PDF).

Also, if some structure doses not exist in the COD, you can find it in the literature, make a CIF out of it and deposit it to the COD – the next COD revision will have it, and hopefully in due time Bruker will upgrade Eva to include it :) (but please don't take records from PDF or other non-open database, this violates copyright).

However, please keep in mind that the scope of the COD and the PDF databases is slightly different:

- the COD collects all crystal structure data, for both organic and inorganic materials

- the PDF started as a collection of powder diffractograms for material identification; thus they have scattering data even in cases when the atomic structure of material is not known, e.g. for clays or amorphous materials. The COD explicitly excludes such data, unless a decent Retveld refinement has been done for the structure.

Hope this helps.

Sincerely,
Saulius

--
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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