[Cod-users] sample cif files

[Saulius Gražulis]

Dear Dr. Masami Kanzaki,

thank you very much for your contribution to COD!

On 2017-01-26 01:29, Masami wrote:On 2017-01-26 01:29, Masami wrote:
> I deposited 3.49 GPa file as well as other two files of 
> higher pressure without encountering the error.

Wonderful, great news! I can confirm that the files are in the database
as expected.

> I have several other failed files, but I know how to 
> edit previously deposited cif, so I will add proper tags to 
> these files, and deposit failed files again by myself.

This should work. If you edit the previously deposited files via the Web
interface http://www.crystallography.net/cod, using the "Manage
depositions" and then "View your depositions" links, then you should be
able to update the deposited structures, adding the
_diffrn_ambient_pressure data item, and after that all new depositions
should succeed.

> Thank you so much.

Don't mention!

> Masami Kanzaki

Sincerely yours,
Saulius


>>
>> Dear Dr. Masami Kanzaki,
>>
>> thank you very much for your information, and your great contribution to
>> COD!
>>
>> On 2017-01-25 10:08, Masami wrote:
>>> I attached two cif files.
>>> "stishovite-2.96GPa.cif” was already deposited to COD (as 1544734.cif).
>>> I can not deposit "stishovite-3.49GPa.cif”, and get 
>>> an error message shown below.
>>> “The file [stishovite-3.49GPa.cif] has (at least some) structures that have been deposited to COD previously in entries
>>> 1544734”
>>>
>>> Actually I deposited 7 cif stishovite files of 1bar, 0.95, 1.99, 2.96, 3.49, 4.55 and 5.17 GPa, 
>>> and only the cif of 3.49 GPa got the error message, and apparently pressure 
>>> difference is smallest for this pair (2.96 and 3.49 GPa). 
>>
>> I have looked at the files you have send me and found your deposited
>> structures in the COD. There reason of the error message is the following:
>>
>> The deposited structure files did not have the _diffrn_ambient_pressure
>> data item in them. Their unit cells, however, were different enough (at
>> least one cell parameter difference was outside the 3*sigma range of the
>> square-added standard deviations of the respective cell parameters), so
>> they all were deposited as different structures. The last structure
>> (stishovite-3.49GPa.cif), however, did not experience that much change
>> in the unit cell compared to the stishovite-2.96GPa.cif file. Since the
>> pressure was not specified in the deposited structure, the new structure
>> was caught as a duplicate. Adding pressure to just the new structure did
>> not help, because the deposited 2.96 GPa structure had no pressure value
>> to compare against, and thus signalled the duplicate anyway.
>>
>> I took my liberty to insert the _diffrn_ambient_pressure values into
>> your deposited structures, taking the pressure values from the title and
>> the mineral name. They now all have their measurement pressure recognised:
>>
>>> saulius at koala Masami Kanzaki/ > codslave 'select file, formula, a, b, c, diffrpressure/1E6 as P, mineral from data where title like "%The crystal structure of stishovite under pressure%"'
>>> +---------+-----------+--------+--------+--------+--------+------------------------+
>>> | file    | formula   | a      | b      | c      | P      | mineral                |
>>> +---------+-----------+--------+--------+--------+--------+------------------------+
>>> | 1544731 | - O2 Si - | 4.1797 | 4.1797 | 2.6669 | 0.0001 | stishovite at 1bar     |
>>> | 1544732 | - O2 Si - | 4.1738 | 4.1738 | 2.6663 |   0.95 | stishovite at 0.95 GPa |
>>> | 1544733 | - O2 Si - | 4.1693 | 4.1693 | 2.6652 |   1.99 | stishovite at 1.99 GPa |
>>> | 1544734 | - O2 Si - | 4.1642 | 4.1642 | 2.6636 |   2.96 | stishovite at 2.96 GPa |
>>> | 1544735 | - O2 Si - | 4.1564 | 4.1564 | 2.6602 |   4.55 | stishovite at 4.55 GPa |
>>> | 1544736 | - O2 Si - |  4.152 |  4.152 |  2.659 |   5.17 | stishovite at 5.17 GPa |
>>> +---------+-----------+--------+--------+--------+--------+------------------------+
>>
>> You should now be able to deposit your last file,
>> stishovite-3.49GPa.cif, without a problem. Could you please check if
>> this is the case? If there are still error messages, please let me know,
>> I'll investigate further.
>>
>> Sincerely yours,
>> Saulius
>>
>> -- 
>> Dr. Saulius Gražulis
>> Vilnius University Institute of Biotechnology, Saulėtekio al. 7
>> LT-10223 Vilnius, Lietuva (Lithuania)
>> fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
>> mobile: (+370-684)-49802, (+370-614)-36366
> 


-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10223 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2234367 / phone (office): (+370-5)-2234353
mobile: (+370-684)-49802, (+370-614)-36366