From jeffery.aguiar at inl.gov  Mon Mar 26 02:44:36 2018
From: jeffery.aguiar at inl.gov (Aguiar, Jeffery A)
Date: Sun, 25 Mar 2018 17:44:36 -0600
Subject: [Cod-bugs] Broken CIF Files
Message-ID: <CACJUPheGLidCi0guZyUga0TzqnEDM5y910TWH4QwXRw3kTxqwQ@mail.gmail.com>

Dear the Open Crystallography Database Team,

We have been recently querying your database and have found inconsistencie
sbroken CIF files.

We have attached a text file identifying those files that are either
missing space group, atom position, or other vital crystallographic
information.

We want to make you aware of these inconsistencies in case there are other
users that like us that are using this database.

Kind regards,
Jeff
Preview attachment BrokenCifs.txt
<https://mail.google.com/mail/u/1/?ui=2&ik=52958a24f7&view=att&th=162558d2a7b73b0a&attid=0.1&disp=safe&realattid=f_jf4oeepj0&zw>
BrokenCifs.txt
<https://mail.google.com/mail/u/1/?ui=2&ik=52958a24f7&view=att&th=162558d2a7b73b0a&attid=0.1&disp=safe&realattid=f_jf4oeepj0&zw>--

*Jeffery A. Aguiar, Ph.D.*
*Principal Scientist*
Idaho National Laboratory
Fuel Design and Development Department
2525 Fremont Ave.
Mail Stop 3870
Idaho Falls, ID  83415
Voice:  (208) 526 2884
Cell: (650) 346 1558
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From grazulis at ibt.lt  Mon Mar 26 10:04:51 2018
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=)
Date: Mon, 26 Mar 2018 10:04:51 +0300
Subject: [Cod-bugs] Broken CIF Files
In-Reply-To: <CACJUPheGLidCi0guZyUga0TzqnEDM5y910TWH4QwXRw3kTxqwQ@mail.gmail.com>
References: <CACJUPheGLidCi0guZyUga0TzqnEDM5y910TWH4QwXRw3kTxqwQ@mail.gmail.com>
Message-ID: <5d0a1dc8-7663-da08-7d15-369f7d464de0@ibt.lt>

Dear Aguiar,

thank you very much for the report!

Unfortunately, I can not access the files you mention since they
apparently reside on you Google account, or on some other inaccessible
server.

Could you please attach these files as regular e-mail attachments, or
publish links on a publicly available server where I can download them
without a login?

Sincerely yours,
Saulius

On 2018-03-26 02:44, Aguiar, Jeffery A wrote:
> Dear the Open Crystallography Database Team,
> 
> We have been recently querying your database and have found
> inconsistencie sbroken CIF files.
> 
> We have attached a text file identifying those files that are either
> missing space group, atom position, or other vital crystallographic
> information.
> 
> We want to make you aware of these inconsistencies in case there are
> other users that like us that are using this database.



-- 
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 jeffery.aguiar at inl.gov  Mon Mar 26 17:08:37 2018
From: jeffery.aguiar at inl.gov (Aguiar, Jeffery A)
Date: Mon, 26 Mar 2018 08:08:37 -0600
Subject: [Cod-bugs] Broken CIF Files
In-Reply-To: <5d0a1dc8-7663-da08-7d15-369f7d464de0@ibt.lt>
References: <CACJUPheGLidCi0guZyUga0TzqnEDM5y910TWH4QwXRw3kTxqwQ@mail.gmail.com>
 <5d0a1dc8-7663-da08-7d15-369f7d464de0@ibt.lt>
Message-ID: <CACJUPhdbCh2wrV_4R4YCTW8anYmxYw2=W9ydwu9a9Pz-9bYMBw@mail.gmail.com>

Dear Salius,

Here is a link to the file:
https://drive.google.com/open?id=13QbEUNvjvm6DpMdSSSGtjVaXWjIA8v_-

Jeff

On Mon, Mar 26, 2018 at 1:04 AM, Saulius Gra?ulis <grazulis at ibt.lt> wrote:

> Dear Aguiar,
>
> thank you very much for the report!
>
> Unfortunately, I can not access the files you mention since they
> apparently reside on you Google account, or on some other inaccessible
> server.
>
> Could you please attach these files as regular e-mail attachments, or
> publish links on a publicly available server where I can download them
> without a login?
>
> Sincerely yours,
> Saulius
>
> On 2018-03-26 02:44, Aguiar, Jeffery A wrote:
> > Dear the Open Crystallography Database Team,
> >
> > We have been recently querying your database and have found
> > inconsistencie sbroken CIF files.
> >
> > We have attached a text file identifying those files that are either
> > missing space group, atom position, or other vital crystallographic
> > information.
> >
> > We want to make you aware of these inconsistencies in case there are
> > other users that like us that are using this database.
>
>
>
> --
> 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
>



-- 
*Jeffery A. Aguiar, Ph.D.*
*Principal Scientist*
Idaho National Laboratory
Fuel Design and Development Department
2525 Fremont Ave.
Mail Stop 3870
Idaho Falls, ID  83415
Voice:  (208) 526 2884
Cell: (650) 346 1558
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From nicolas.massoni at cea.fr  Wed Mar 28 16:05:38 2018
From: nicolas.massoni at cea.fr (MASSONI Nicolas)
Date: Wed, 28 Mar 2018 13:05:38 +0000
Subject: [Cod-bugs] Need help to deposit data : one error in the CIF file
Message-ID: <E0D9BC889E6B984B8019FFFF7A01761753DD0C75@EXDAG0-B2.intra.cea.fr>

Hello,

I am trying to deposit an already published data in 2016 (https://doi.org/10.1107/S2056989016014225). Attached is the uploaded CIF file. But the system finds the following warning : "unallowed symbol in CIF comment". Please I need some assistance to skip this warning to complete the deposition process. Thanks

Best regards

Nicolas

----------------------------------------------------------------------------------------------------------
Nicolas Massoni
CEA Marcoule DE2D-SEVT, LCV
BP17171 30207 Bagnols/C?ze Cedex
T?l 04 66 79 18 05 Fax 04 66 79 18 80

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From grazulis at ibt.lt  Wed Mar 28 16:33:22 2018
From: grazulis at ibt.lt (=?UTF-8?Q?Saulius_Gra=c5=beulis?=)
Date: Wed, 28 Mar 2018 16:33:22 +0300
Subject: [Cod-bugs] Need help to deposit data : one error in the CIF file
In-Reply-To: <E0D9BC889E6B984B8019FFFF7A01761753DD0C75@EXDAG0-B2.intra.cea.fr>
References: <E0D9BC889E6B984B8019FFFF7A01761753DD0C75@EXDAG0-B2.intra.cea.fr>
Message-ID: <6a226f3f-44cd-e3a2-e6a2-f35fdcb17470@ibt.lt>

On 2018-03-28 16:05, MASSONI Nicolas wrote:
> ?
> 
> I am trying to deposit an already published data in 2016
> (https://doi.org/10.1107/S2056989016014225). Attached is the uploaded
> CIF file. But the system finds the following warning : ?unallowed symbol
> in CIF comment?. Please I need some assistance to skip this warning to
> complete the deposition process. Thanks

Dear Nicolas,

thank you very much for depositing your data to COD!

The file you have attached is fine at the moment and no longer contains
special symbols (our deposition pipeline has filtered them away). The
workaround in the COD deposition web site for the message you quote
would be to click on "Edit" button, and them immediately click on
"Save". I realise that this is an inconvenience and we'll see if we can
fix the Web site so that this message no longer precludes deposition.

There is one more nuance in the file you have provided: author names
should not be written in one line ('Massoni, Nicolas and Pierrick,
Chevreux') but as two separate strings in a loop:

> loop_
> _publ_author_name
> 'Massoni, Nicolas'
> 'Pierrick, Chevreux'

I also suggest adding DOI ? this will make us easier to track back the
publications. Please find an updated file with these changes attached.
The file should be accepted by the COD deposition system.

Sincerely yours,
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
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From antanas.vaitkus90 at gmail.com  Wed Mar 28 16:41:08 2018
From: antanas.vaitkus90 at gmail.com (Antanas Vaitkus)
Date: Wed, 28 Mar 2018 16:41:08 +0300
Subject: [Cod-bugs] Need help to deposit data : one error in the CIF file
In-Reply-To: <6a226f3f-44cd-e3a2-e6a2-f35fdcb17470@ibt.lt>
References: <E0D9BC889E6B984B8019FFFF7A01761753DD0C75@EXDAG0-B2.intra.cea.fr>
 <6a226f3f-44cd-e3a2-e6a2-f35fdcb17470@ibt.lt>
Message-ID: <CALHYoX7TVVzgPctS2=17UObZsCm4NEpO6hen-DNeEX6gCE75gA@mail.gmail.com>

Dear Nicolas Massoni,

Saulius' comments are correct, however, there seems to be an additional
problem on our side that prevents the "Edit"->"Save" approach from working.

We will try to issue a bug-fix as soon as possible and will inform You once
it is done.

Sincerely,
Antanas Vaitkus

2018-03-28 16:33 GMT+03:00 Saulius Gra?ulis <grazulis at ibt.lt>:

> On 2018-03-28 16:05, MASSONI Nicolas wrote:
> >
> >
> > I am trying to deposit an already published data in 2016
> > (https://doi.org/10.1107/S2056989016014225). Attached is the uploaded
> > CIF file. But the system finds the following warning : ?unallowed symbol
> > in CIF comment?. Please I need some assistance to skip this warning to
> > complete the deposition process. Thanks
>
> Dear Nicolas,
>
> thank you very much for depositing your data to COD!
>
> The file you have attached is fine at the moment and no longer contains
> special symbols (our deposition pipeline has filtered them away). The
> workaround in the COD deposition web site for the message you quote
> would be to click on "Edit" button, and them immediately click on
> "Save". I realise that this is an inconvenience and we'll see if we can
> fix the Web site so that this message no longer precludes deposition.
>
> There is one more nuance in the file you have provided: author names
> should not be written in one line ('Massoni, Nicolas and Pierrick,
> Chevreux') but as two separate strings in a loop:
>
> > loop_
> > _publ_author_name
> > 'Massoni, Nicolas'
> > 'Pierrick, Chevreux'
>
> I also suggest adding DOI ? this will make us easier to track back the
> publications. Please find an updated file with these changes attached.
> The file should be accepted by the COD deposition system.
>
> Sincerely yours,
> 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
>
> _______________________________________________
> Cod-bugs mailing list
> Cod-bugs at lists.crystallography.net
> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>
>


-- 
Antanas Vaitkus,
PhD student at Vilnius University Institute of Biotechnology,
room V325, Saul?tekio al. 7,
LT-10257 Vilnius, Lithuania
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From andrius.merkys at gmail.com  Wed Mar 28 17:19:19 2018
From: andrius.merkys at gmail.com (Andrius Merkys)
Date: Wed, 28 Mar 2018 17:19:19 +0300
Subject: [Cod-bugs] Need help to deposit data : one error in the CIF file
In-Reply-To: <E0D9BC889E6B984B8019FFFF7A01761753DD0C75@EXDAG0-B2.intra.cea.fr>
References: <E0D9BC889E6B984B8019FFFF7A01761753DD0C75@EXDAG0-B2.intra.cea.fr>
Message-ID: <6c94b93e-57f0-5a48-7871-6a24334bca5d@gmail.com>

Dear Nicolas,

we have resolved the problem, please continue with the deposition. Thank you for letting us know about the issue.

Best wishes,
Andrius

On 03/28/2018 04:05 PM, MASSONI Nicolas wrote:
>
> Hello,
>
> ?
>
> I am trying to deposit an already published data in 2016 (https://doi.org/10.1107/S2056989016014225). Attached is the uploaded CIF file. But the system finds the following warning : ?unallowed symbol in CIF comment?. Please I need some assistance to skip this warning to complete the deposition process. Thanks
>
> ?
>
> Best regards
>
> ?
>
> Nicolas
>
> ?
>
> ----------------------------------------------------------------------------------------------------------
>
> Nicolas Massoni
>
> CEA Marcoule DE2D-SEVT, LCV
>
> BP17171 30207 Bagnols/C?ze Cedex
>
> T?l 04 66 79 18 05 Fax 04 66 79 18 80
>
> ?
>
>
>
> _______________________________________________
> Cod-bugs mailing list
> Cod-bugs at lists.crystallography.net
> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs

-- 
Andrius Merkys
Vilnius University Institute of Biotechnology, Saul?tekio al. 7, room V325
LT-10257 Vilnius, Lithuania

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