From andrius.merkys at gmail.com  Tue Jun 25 12:14:10 2019
From: andrius.merkys at gmail.com (Andrius Merkys)
Date: Tue, 25 Jun 2019 12:14:10 +0300
Subject: [Cod-bugs] Fwd:  information card for entry 1524837
In-Reply-To: <alpine.DEB.2.21.1904230825340.3637@orion>
References: <alpine.DEB.2.21.1904230825340.3637@orion>
Message-ID: <7ae4553e-0fc3-dac3-159f-3462937c82f4@gmail.com>

Dear Advisory Board,

A couple of months ago (sorry for holding it for so long) I have
received the following email describing a throughout analysis of a COD
entry of a structure published in 1938. The authors have compared the
structure and its simulated powder pattern to the similar structures in
the PDF database, and drew a conclusion that the structure in the COD
should be fixed. I am a little hesitant to modify the CIF, but what do
others think? Is the evidence sufficient to fix the CIF, or does the
original structure make sense enough to keep it?

In the meantime I will thank the authors for their detailed report in a
separate email.

Best wishes,
Andrius


-------- Forwarded Message --------
Subject: 	Re: [Cod-bugs] information card for entry 1524837
Date: 	Tue, 23 Apr 2019 08:42:34 -0500 (CDT)
From: 	Evgeni Penev <esp1 at rice.edu>
To: 	cod-bugs at ibt.lt
CC: 	Nitant Gupta <nitant.gupta at rice.edu>, Boris I. Yakobson
<biy at rice.edu>, kb13 at rice.edu




Dear COD Team,

We're writing regarding the information card for entry 1524837 (formula:
Co7W6). Based on the detailed analysis we have carried out in our recent
publication [1] and comparison with other sources [2], including the
original paper [3] referenced on the COD page, we believe that the
structure as provided in the 1524837.cif file is incorrect.

We have identified the problem to be an erroneous entry for the 18(h)
Wyckoff position in hexagonal axes [respectively, 6(h) in rhombohedral
axes]:
...
Co2 Co 0.8065 0.613 0.203 1 0.0
...
This line should read:
Co2 Co -0.16667 -0.3333 0.2567 1 0.0
in accordance with Ref. [3].

The incorrect structure can be recognized in a number of publications,
including, but not limited to:
-- F. Yang et al., Nature 510, 522 (2014)
-- F. Yang et al., J. Am. Chem. Soc. 137, 8688 (2015)
-- F. Yang et al., Acc. Chem. Res. 49, 606 (2016)
-- F. Yang et al., ACS Nano 11, 186 (2017)
-- F. Yang et al., J. Am. Chem. Soc. 141, 5871 (2019)
possibly affecting the interpretation of experimental and theoretical
results and the conclusions reached by the authors. We do not, however,
express opinion as to how/if the COD entry 1524837 is related to the
above publications.

We will appreciate it if you can fix this entry, including a clear
comment to make any users aware of this important flaw.


Sincerely,
Evgeni Penev, Ksenia Bets, Nitant Gupta, Boris Yakobson


***


[1] E. S. Penev, K. V. Bets, N. Gupta, and B. I. Yakobson, Nano Lett.
18, 5288 (2018); see Supporting Information, Sections S1 and S2,
https://pubs.acs.org/doi/suppl/10.1021/acs.nanolett.8b02283

[2] S. Curtarolo, W. Setyawan, S. Wang, J. Xue, K. Yang, R. H. Taylor,
L. J. Nelson, G. L. Hart, S. Sanvito, M. Buongiorno-Nardelli, N. Mingo,
and O. Levy, Comp. Mater. Sci. 58, 227 (2012), AFLOW id:
7c14e45740f66a35, http://materials.duke.edu/AFLOWDATA/LIB2_RAW/CoW_pv/613/

[3] A. Magneli, and A. Westgren,




--
Evgeni S. Penev, PhD
Assistant Research Professor
Rice University
MSNE Dept - MS 325
Houston, TX 77005-1827
sites.google.com/site/evgenispenev
_______________________________________________
Cod-bugs mailing list
Cod-bugs at lists.crystallography.net
http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
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From grazulis at ibt.lt  Tue Jun 25 12:24:26 2019
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=)
Date: Tue, 25 Jun 2019 12:24:26 +0300
Subject: [Cod-bugs] Fwd: information card for entry 1524837
In-Reply-To: <7ae4553e-0fc3-dac3-159f-3462937c82f4@gmail.com>
References: <alpine.DEB.2.21.1904230825340.3637@orion>
 <7ae4553e-0fc3-dac3-159f-3462937c82f4@gmail.com>
Message-ID: <6feeb625-1cd1-88d8-5f0c-8a13737f6edb@ibt.lt>

On 2019-06-25 12:14, Andrius Merkys wrote:
> A couple of months ago (sorry for holding it for so long) I have
> received the following email describing a throughout analysis of a COD
> entry of a structure published in 1938. The authors have compared the
> structure and its simulated powder pattern to the similar structures in
> the PDF database, and drew a conclusion that the structure in the COD
> should be fixed. I am a little hesitant to modify the CIF, but what do
> others think? Is the evidence sufficient to fix the CIF, or does the
> original structure make sense enough to keep it?

I think the current policy would be to keep the COD entry, but to
remediate data according to the situation.

a/ if the original paper (if someone has a PLS, pls. share) has
*correct* coordinates, we should fix the entry and issue a new revision;

b/ if the coordinates are wrong in the original paper, we should mark
the COD entry 1524837, and add information about (linkers to) the
correct redeterminations of the structure in question. I would add
_cod_error_flag errors _cod_error_source publication to the 1524837.cif
in that case.

There is also one more sch structure, from Wyckoff, with corrections
published I guess by Pauling; I do not have the file entry handy for
now. We should follow the same procedure.

> In the meantime I will thank the authors for their detailed report in a
> separate email.

Yes, we should do that.


-- 
Dr. Saulius Gra?ulis
Vilnius University Institute of Biotechnology, Saul?tekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
mobile: (+370-684)-49802, (+370-614)-36366


From grazulis at ibt.lt  Tue Jun 25 12:27:35 2019
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=)
Date: Tue, 25 Jun 2019 12:27:35 +0300
Subject: [Cod-bugs] Fwd: information card for entry 1524837
In-Reply-To: <7ae4553e-0fc3-dac3-159f-3462937c82f4@gmail.com>
References: <alpine.DEB.2.21.1904230825340.3637@orion>
 <7ae4553e-0fc3-dac3-159f-3462937c82f4@gmail.com>
Message-ID: <13c0ef2b-4193-5418-e195-67994433b05b@ibt.lt>

On 2019-06-25 12:14, Andrius Merkys wrote:
> COD entry of a structure published in 1938

And these data come from the same dubbious source:

> saulius at koala ~/ $ grep _cod_data_source_file $(codid2file 1524837)
> _cod_data_source_file            Magneli_ZAACAB_1938_1266.cif

I mean, the input file name is a tell-tale sign of the strange multiple
structure deposition event... you know what I am talking about.

:/ ...

I guess there is a need to reinvestigate all these structures more closely.

Regards,
Saulius

-- 
Dr. Saulius Gra?ulis
Vilnius University Institute of Biotechnology, Saul?tekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
mobile: (+370-684)-49802, (+370-614)-36366