[Cod-bugs] "No data blocks that contain coordinates found"

Wed Oct 4 09:40:54 EEST 2017

Dear Amanda,

the requirements are indeed a bit misleading -- neither of the repositories
recommended by the "Crystals" journal (COD, CSD) accept crystal structures
of proteins. I would assume that the PDB was accidentally omitted in the
recommendations on the basis that depositing protein structures to the PDB
prior to publication has become a *de facto* standard nowadays. I will
write an e-mail to the "Crystals" editorial board asking them to update the
instructions.

As for now, I would assume that the best solution for you would be to
deposit your data to the PDB and simply reference it in the paper.

Sincerely,
Antanas Vaitkus

2017-10-03 18:29 GMT+03:00 Amanda Constantinides <
aconstantinides1 at student.gsu.edu>:

> This is what is on the website:http://www.mdpi.com/
> journal/crystals/instructions
>
> *"X-Ray Crystallographic Data:**Crystals**deposit the crystallographic
> data prior to the submission of the manuscript*
>
>    - *COD:* Preferably, the data should be deposited with the Crystallography
>    Open Database (COD) <http://www.crystallography.net/>. Please deposit
>    as "pre-publication data" at http://www.crystallography.
>    net/initiate_deposition.php prior to the submission of the manuscript.
>    COD numbers for structures will be displayed immediately after the data is
>    validated and deposited, and should be included in the manuscript, along
>    with the following text: "COD ...... contains the supplementary
>    crystallographic data for this paper. These data can be obtained free of
>    charge via http://www.crystallography.net/search.html". This text may
>    be included in the experimental section or as a suitably referenced
>    endnote."
>
> I am not sure how I have misinterpreted this.
>
> Best,
>
> Amanda Constantinides
>
> <http://www.mdpi.com/journal/crystals/instructions>
> Crystals | Instructions for Authors
> <http://www.mdpi.com/journal/crystals/instructions>
> www.mdpi.com
> Crystals, an international, peer-reviewed Open Access journal.
>
>
>
> ------------------------------
> *From:* Amanda Constantinides
> *Sent:* Tuesday, October 3, 2017 11:26:38 AM
> *To:* Antanas Vaitkus
>
> *Subject:* Re: [Cod-bugs] "No data blocks that contain coordinates found"
>
>
> Hi Antanas,
> Ohhhh ok!!! I must have misread the directions for submission in the
> journal *Crystals*. I was also wondering why the PDB was not sufficient
> for this journal. I will check the directions again.
>
>
> Thank you!
>
> Amanda Constantinides
> ------------------------------
> *From:* Antanas Vaitkus <antanas.vaitkus90 at gmail.com>
> *Sent:* Tuesday, October 3, 2017 9:30:11 AM
> *To:* Amanda Constantinides; cod-bugs at ibt.lt
> *Subject:* Re: [Cod-bugs] "No data blocks that contain coordinates found"
>
> Dear Amanda,
>
> am I correct to assume that You are trying to deposit a protein crystal
> structure? The scope of the COD does not include biopolymers since this
> domain is already well covered by the PDB database.
>
> Is there any reason not to deposit your crystal structure to the PDB
> database?
>
> Sincerely,
> Antanas Vaitkus
>
> 2017-10-03 14:13 GMT+03:00 Amanda Constantinides <
> aconstantinides1 at student.gsu.edu>:
>
>> Hi Antanas,
>> I can not send any data. It is not published yet. I have a regular PDB
>> file, an .mtz file, a log file (.lp), and a .sca file. What is the best way
>> to convert them to .cif format to be uploaded into the COD? My attempt
>> using PDB_extract was not successful.
>>
>> Thank you,
>>
>> Amanda Constantinides
>> ------------------------------
>> *From:* Antanas Vaitkus <antanas.vaitkus90 at gmail.com>
>> *Sent:* Monday, October 2, 2017 3:12:36 PM
>> *To:* Amanda Constantinides
>> *Cc:* cod-bugs at ibt.lt
>> *Subject:* Re: [Cod-bugs] "No data blocks that contain coordinates found"
>>
>> Dear Amanda Constantinides,
>>
>> thank you for taking interest in the COD. Could you please send an
>> example of the CIF files you are trying to upload so we could investigate
>> further?
>>
>> Sincerely,
>> Antanas Vaitkus
>>
>> 2017-10-02 20:30 GMT+03:00 Amanda Constantinides <
>> aconstantinides1 at student.gsu.edu>:
>>
>>> Hi,
>>>
>>> I am trying to deposit several structures in the COD in preparation for
>>> publication in *Crystals*. I used PDB_extract to convert structure
>>> factor and coordinate files to .CIF format. When I tried to upload either
>>> of these compressed CIF files, the error message "no data blocks that
>>> contain coordinates found" came up. When I tried to add diffraction data
>>> files (.mtz files with .lp files converted to .cif files in PDB_extract),
>>> new error messages came up.
>>>
>>> How can I deposit these structures?
>>>
>>> Thank you,
>>>
>>> Amanda Constantinides
>>> Graduate Research Assistant
>>> Georgia State University
>>>
>>>
>>>
>>> _______________________________________________
>>> Cod-bugs mailing list
>>> Cod-bugs at lists.crystallography.net
>>> http://lists.crystallography.net/cgi-bin/mailman/listinfo/cod-bugs
>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.crystallography.net%2Fcgi-bin%2Fmailman%2Flistinfo%2Fcod-bugs&data=02%7C01%7Caconstantinides1%40student.gsu.edu%7Ce906b436ad8049b10d6308d509c98bd7%7C704d822c358a47849a1649e20b75f941%7C0%7C0%7C636425683594580764&sdata=3HmT8D4H1I%2Bqhm0WEok%2BsH0fFs7tGb7oyeqAPy5oXEA%3D&reserved=0>
>>>
>>>
>>
>>
>> --
>> Antanas Vaitkus,
>> PhD student at Vilnius University Institute of Biotechnology,
>> room V325, Saulėtekio al. 7
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaps.google.com%2F%3Fq%3DSaul%25C4%2597tekio%2Bal.%2B7%26entry%3Dgmail%26source%3Dg&data=02%7C01%7Caconstantinides1%40student.gsu.edu%7Ccbd7d6dfba414408cc0a08d50a62e07b%7C704d822c358a47849a1649e20b75f941%7C0%7C0%7C636426342139278837&sdata=dOUd8nR%2B0yZMZRrtT0l1ExrXJ5s8LJhiSfe7JFhKX8A%3D&reserved=0>
>> ,
>> LT-10257 Vilnius, Lithuania
>>
>>
>>
>
>
> --
> Antanas Vaitkus,
> PhD student at Vilnius University Institute of Biotechnology,
> room V325, Saulėtekio al. 7
> <https://maps.google.com/?q=Saul%C4%97tekio+al.+7&entry=gmail&source=g>,
> LT-10257 Vilnius, Lithuania
>
>
>

-- 
Antanas Vaitkus,
PhD student at Vilnius University Institute of Biotechnology,
room V325, Saulėtekio al. 7,
LT-10257 Vilnius, Lithuania
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