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@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