Incommensurate Structure Database
New Structure
The data for the incommensurate structures is saved in text files using the CIF format.
For each structure there is one CIF file containing all of the information.
This permits different ways of adding a structure to the database:
- e-mail submition:
you can send us a CIF file for the structure which has
been already prepared with some program.
- If you have a CIF file obtained using the
program system Jana
you can submit it to the database using the Jana2ICSDB
form for
giving the information that is not included in the output of Jana but is
necessary for the structures in the database as the name(s) of the author(s),
publication data, experimental data and e-mail for contact.
- Also, the web interface for the structure input can be used.
In this case you have to pass through different forms giving the corresponding
information and the CIF file will be generated for you.
When the structure is submitted to the database it is assigned an ID
and you are asked for a password. This way you can edit the data giving the ID and
the password. Any information related with the change in the data for the structure
will be send to an e-mail given as _publ_contact_author_email in the
CIF file or as e-mail for contact in the form with the general information,
when the web interface is used.
Please, note when you send a CIF file it should contain all of the information
that would have been given if you have used the web interfase. Nevertheless, it can contain
more data items. These items will not be shown when the data for the structure is presented.
In the case of composite structures there are two posibilities for describing the structure:
- W-matrix description when the data for the subsystems is given at the same time
specifying for each atom site which subsystem it belongs to.
- Subsystems description when the data for each one of the subsystems is given
separately as if it were a modulated structure.
Depending on the type of the description of the composite the form of the
CIF files is different.
When W-matrices are used to describe the composite
the CIF file contains three blocks corresponding to the
general data, average structure data (if the average structure has been refined
separately) and modulated structure data. Anywhere in the CIF file where a data for
an atom site is given the subsystem this atom site belongs to have to be specified.
If the subsystems descritpion is choosen than there is one block with the common information
for all of the subsystems and different blocks for each subsystem in the CIF file.
Thus, the subsystem an atom site belongs to is specified by the block this site is listed into.
The data for the structures is saved in CIF files so
all of the values have to be given in accordance with the CIF format.
The format of the greek symbols, subscripts, superscripts and special symbols is the one
described in
The Crystallographic Information File (CIF): a New Standard Archive File for
Crystallography, Sydney R. Hall, Frank H. Allen, and I. David Brown,
Acta Cryst. A 47, 655-685 (1991)
This is the first step in giving a new structure. In the first part named ``Compound'',
the formula and the number of the atom sites are the obligatory data that have to be given.
The number of the atom sites can be changed subsequently.
If the structure is published the name, volume, and the pages of the article,
in the form (first_page - last_page), have to be given.
The part ``Experimental Data''asks for the information about the temperature in Kelvins
at which the intensities have been measured, the type of radiation used, the number
of the satellites and details about the refinement.
The part related with the ``Overall phason correction'' asks for the formula and the value
of the coefficient used to calculate the overall phason correction.
Also, you have to specify if the average structure separately refined using
the main reflections.
If so, you have to give the data for the average structure, too.
The obligatory items from the general data are:
- the formula;
- the number of the independent atoms;
- the name and e-mail for contact: Note, the e-mail address you give will be
used to inform you about changes made on the structure data, so please,
give valid e-mail address;
- the maximal order of satellites.
- for the case of composites it is obligatory t ogive aslo the number of the
subsystems and the dimension of the modulation
After the general information is given you have to click over
the button [Submit General Information] in order to save this information.
This will show a page with the data already given and the
button [Modulated Structure Data]. In the case that the
average structure is determined separately there is a button
[Average Structure Data], too.
When the structure is a composite, there is a button
[W matrices], too.
Also, there will be an empty fields to give a password for the structure.
This password and the ID assigned to the structure when the general information is submitted
are used later to edit the data, already given, once the structure is submitted to the
database, or to continue entering the structure if, for some reason, you have enter only
a part of the data and have not submitted the structure to the database.
The order of the giving the rest of the data is not important, so you can choose
which data to give next by clicking over the corresponding button.
To edit the general data click over the button [Edit General Information].
This will show you a form with the values that you have been given
so you can change them and save the new data using the
[Submit General Information] button.
Description of the data items
When the average structure is determined independently the data concerning
this structure have to be given apart from that for the modulated structure.
This section asks for the information about:
For the data that is not known you can leave the empty value or put "?".
To save the data click over the button [Submit Average Structure].
PLEASE NOTE: If you go back with the "Back" button of your browser
the data you have been given will not be saved.
To save the data click on the button [Submit Average Structure].
This will show the data that you have been given in a HTML format and will
save it in a temporary CIF file.
To edit this data click on [Edit Average Structure].
To edit the data for the modulated structure click on the button
[Modulated Structure] and for the general data use the button
[General Data].
The form for the modulated structure data asks for:
To save the information click on the button [Submit Modulations]
This will show you the data that you have been given. To edit this data click over
[Edit Modulations].
After the modulate structure information is given the modulation parameters can be
entered by clicking over the button [Modulation Parameters].
The information about the modulation parameters have to be given in two steps:
- At the first one the information about the
modulation function, number of the wave vectors used in the description
of the modulation, number of measured wave vectors, and the method,
used for the calculation of the structure factors have to be specified.
Also, for each one of the atom sites, the type of the modulation and the
function, used to describe it, have to be selected.
To save this information and pass to the step two, click over
[Atom Sites Modulation].
- After the data listed above are saved by clicking over [Atom Sites Modulation]
you have to give the coordinates for the wave vectors and
the values of the parameters for the modulation functions for each one of the atoms
and each one of its modulations.
To save the data click over [Submit Modulations]. This will show you
the list with the data you have already been given. To edit this data
click over [Edit Modulation Parameters].
To edit general information click over
[General Structure Data] and for the modulated structure data use
[Modulated Structure Data]
Description of the data items
In the case of composites as a part of the common information have to be given the marices
Wi which relate the bases of the different subsystems. Also, this is the place
to give the codes and the descritpions of the subsystems. These codes will be used later
when it is necessary to specify the subsystem (for example when the atom sites data is given).
Description of the data items
Submitting the Structure
When all of the data is given you can click over [All Structure]
to view all of it in the form it will appear when the structure is added
to the database and someone asks for all information.
If the data given seems to be correct you can submit the structure to the database
by clicking over [Save the Structure].
After the structure is submitted to the database, you will be sent an e-mail with the
structure ID and the structure is checked using the
program system Jana.
The result from this check is send to the author gievn as author for contact
in the part with the General Information.
You can edit the structure using the link Edit a structure from the
main page of ICSDB,
and giving the ID and the password you have given during the input of the structure data.
[ICSDB Main Menu]
Please send your comments about this site to:
cryst@wm.lc.ehu.es
