[Cod-bugs] depositing "duplicates"

Antanas Vaitkus antanas.vaitkus90 at gmail.com
Mon Jun 21 22:05:44 EEST 2021

Dear Erik Rakovsky,

CIF files that are acquired from the same data using different refinement
are normally handled by marking one the structures (the best one in your
as the optimal and the rest are marked as suboptimal ones. This markup
us to automatically exclude the suboptimal structures from database-wide
calculations and in doing so not overrepresent a single structure (in some
extreme cases the same structure may contain several tens of models).

For now, let's assume that the CIF file that you have already uploaded is
the optimal
one. This can easily be changed later. To successfully deposit the rest of
the CIF files,
you should add the following two lines to each of the other CIF files:

_cod_related_optimal_entry_code  3000306
_cod_suboptimal_structure        yes

The first line states that the entry that you have already deposited (COD
ID 3000306 [1])
is the optimal one and the second line simply states that the given
structure is a suboptimal
one (in general). The deposition website will complain about the
data item not being recognised, but just ignore it -- it is a minor known
bug in our system.

Does this seem reasonable? If entry 3000306 is not the optimal one, just
let me know and
I can change it manually after you deposit the rest of the structures.

[1] https://www.crystallography.net/cod/3000306.html

Please let us know if this works for you.

Antanas Vaitkus

On Mon, 21 Jun 2021 at 21:31, Rakovský Erik <erik.rakovsky at uniba.sk> wrote:

> Hello Anatas & co. 🙂
> so my problem in short is that I need to have deposited 4 structures of
> the same compound and the same polymorph but refined using several
> strategies. The results/differences will be thoroughly discussed in the
> article.
> For example
>    - "routine" refinement with geometrically placed hydrogens, X-H
>    distances fixed in default distances, Uiso(H) riding (1.2 or 1.5 times Ueq
>    of parent atom)
>    - the same strategy but X-H distances free to refine and even Uisos
>    can be sometimes refined freely, too
>    - Hirshfeld atom refinement using several methods (HF/DFT, various
>    basis sets or functionals) - in my case, I used two different basis sets
>    for final two refinements
> originally I described the refinement using
> _olex2_refinement_description
> ;
> HAR refinement using NoSpherA2/ORCA
> def2-TZVPP basis set
> PBE0 functional
> integration accuracy Max
> SCF Threshold VeryTightSCF
> SCF Strategy VerySlowConv
> ;
> any idea how to do this without the exploit of _chemical_compound_source
> or other tag?
> Best regards,
> Erik Rakovsky
> --
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Antanas Vaitkus,
PhD student at Vilnius University Institute of Biotechnology,
room V325, Saulėtekio al. 7,
LT-10257 Vilnius, Lithuania

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