[Cod-bugs] COD to PDF

[Saulius Gražulis]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20200225/00970026/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: grazulis.vcf
Type: text/x-vcard
Size: 4 bytes
Desc: not available
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20200225/00970026/attachment.vcf>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 213 bytes
Desc: OpenPGP digital signature
URL: <http://lists.crystallography.net/pipermail/cod-bugs/attachments/20200225/00970026/attachment.sig>