Quick guide on Using Structure Type Descriptor Searches

Structure Type Descriptor Search

For a structure type search, a new button Advanced Options was added to the Reference tab.
Please note that this button is only displayed if you select Structure Type in the left-hand list (see
Fig. 1).


Fig. 1: Button "Advanced Options" on Reference tab.


Click the Advanced Options button to get a new pop-up window (Fig. 2).


Fig. 2: Window for detailed structure type search.


Users can enter search text into text boxes for space group number, space group symbol, Wyckoff
sequence, Pearson symbol, ANX formula, c/a ratio, and beta (Fig. 3). A list of available items will be
generated for the current selection.
Please also note that the selection (and search) can be done in either the authors data, or the
standardized data, or both. The default is to search in both sets of data.


Fig. 3: Structure types can be searched by their defining descriptors. Please note that c/a ratios and beta angles are not used
to refine the search.


Select an item in the list boxes or enter a space group number, c/a ratio, or beta range to create the
selection criteria. All the list boxes will be updated at the same time, based on the criteria; the Pre-
defined Structure Types will display structure type formulas that meet the criteria (Fig. 4).
Note: The table structure_type is used to create the list of formulas (with some modifications of the
criteria). The c/a ratio and beta range are not used either when searching for the pre-defined structure
types.


Fig. 4: Structure type descriptors are selected in the list boxes. The list boxes display all space groups, Wyckoff sequences,
Pearson symbols and ANX formulas for which a structure exists in the database with the currently selected criteria. This
does not necessarily have to be one of the defined structure types.







The user has two options to create search criteria for the actual database search in FindIt. The first is to
use the selected descriptor sets, which includes all selected list box descriptors in the search. The
second is to use the selected pre-defined structure type formula(s), which will search those structure
types. To search for the structure type descriptor set, click on the Search on Descriptors button; to
search for the formula, click on the Search on Selected Structure Type Formula button (Fig. 5). The
pop-up window will be closed and the user is redirected to the main search window of FindIt.


Fig. 5: Criteria for the search can be transferred to the FindIt main window by using the "Search on Descriptors" button or
the "Search on Selected Structure Type Formula" button.







Clicking on Search on Selected Structure Type Formula will have the same effect as selecting a
formula in the original structure type search frame. The selected formula will be highlighted, and the
search text will display the formula(s)(Fig. 6).


Fig. 6: FindIt main window after using the "Search on Selected Structure Type Formula" button.

By clicking on Search on Descriptors, the search text will be displayed as STYPE[User Criteria] (Fig.
7). To modify the searching criteria, or to switch between formula search and descriptor search, click on
the Advanced Options button again.


Fig. 7: FindIt main window, after using the "Search on Descriptors" button.

Note: A search can be conducted in the database on authors data and/or standardized data for the
descriptor set criteria. The only place to determine where the search will be conducted is in the pop-up
window.



Notes on the Structure Type Descriptor set search (Advanced Options)

The design of the interface allows two ways of setting criteria for structure type searching:

1) a combination of space group number/symbols, Pearson, Wyckoff, ANX formula, c/a ratio
and beta range;
2) structure type formula (which is displayed based on certain criteria in the structure type
descriptor set).

However, 1) and 2) do not necessarily cover the same set of entries, even though they are displayed
and updated at the same time; and the definitions displayed in 2) may not be consistent with 1).

The following may explain the apparent inconsistencies:

a. There are ~35,000 entries without assigned structure types. It is possible that when the user
chooses the descriptor set, there are database entries that meet the criteria, but there is no
structure type formula to be displayed.

b. The definitions of the structure type formula may be based on authors data or standardized
data. If the authors data are not exactly the same as the standardized data, the descriptor set
searching results may differ if the user is not searching on both authors and standardized data.

On the other hand, descriptor set searching may return entries with structure type formula(s)
that are not displayed in the form. For example, if the user selects space group symbol P1,
Wyckoff a13, there will be no structure type formula displayed. However, searching
standardized data will return entries with structure type Al2SiO5(OH)4 assigned, which is
defined as space group symbol C1, Wyckoff a13, and Pearson aP17, (using authors
data).

c. Each unique structure type formula may have multiple structure type descriptor sets associated
with it. For example:

STRUCT_TYPE SGR WYCK PEARSON CA_MIN CA_MAX SGR_NUM
NaxV2O5 A12/m1 i11 a mS44 1.47 1.62 12
NaxV2O5 C12/m1 i11 a mS44 .6 .68 12
NaxV2O5 C12/m1 j i11 a mS44 .6 .68 12






Quick guide on Using Structure Tidy

Starting Structure Tidy

As exactly one entry is selected from the search results, a new button will be enabled on the toolbar
(the distance calculation button operates the same way) (Fig. 8).


Fig. 8: The Structure Tidy icon is only enabled if exactly one entry is selected in the search results.


Click the button to run Structure Tidy (note that the first time the program is run, it may take a long time
to launch). A progress bar will then appear before the program finishes processing the input and
reading the output generated by Structure Tidy (Fig. 9). A new window will then pop up with the input
and output data allowing you to edit the input data and to rerun the program.



Fig. 9: Structure Tidy runs in the background and the output is read into the ICSD Standardization window.

Further details about the ICSD Standardization window

Input and output

There are two panels on the window; the panel on the left displays input data, and the panel on the
right displays output data (Fig. 10).


Fig. 10: Description of the ICSD Standardization window. On the left the input data are displayed and on the right the output
is given.
Tidy input and output text can also be found in the Read Input Text (Fig. 11, left) and Read Output
Text (Fig. 11, right) tabs in the right panel.


Fig. 11: The input for Structure Tidy can seen on the Read Input Text tab in the left-hand panel. The output can be
displayed in the right-hand panel using the Read Output Text tab .

The user can edit input data in the panel on the left side and click the Update Standardization button
to run Structure Tidy and update the output.

Alternatively, the user can modify the Structure Tidy input text directly and run the program by clicking
the Update and Run button (Fig. 12) without using the interface to do any interpretation and
modification.

Using the interface can help to check the text and make modifications that are necessary in order to
avoid some limitations in the Structure Tidy program. To do so, click on Update Only to update the
input panel, and run Update Standardization from there (Fig. 12).


Fig. 12: There are two ways to run Structure Tidy from the interface.



Origin choice and Polar group

If the specified space group number has origin choice options or is a polar space group, the choice of
origin and the option to allow Structure Tidy to calculate the best origin will be enabled (Fig. 13).


Fig. 13: Different origin choices are possible for some space groups.

Dummy sites

Dummy sites are displayed with a > symbol (for example, see QA in Fig. 14). For the ICSD entries,
the convention used is that all the dummy sites names start with Q and are followed by another
alphabetic letter.

To display the definition of the dummy site, point the mouse to the atom name. A yellow balloon will
appear with the definition (Fig. 14).


Fig. 14: The definition of a specific dummy site can be displayed by pointing the mouse to the atom name.


The definition of the dummy sites can be changed by clicking Edit Dummy Sites button in the toolbar,
or by right-clicking on the grid and selecting Edit Dummy Sites in the menu (Fig. 15).



Fig. 15: Open the Dummy Sites pop-up window either by using an icon in the toolbar or by right-clicking on the grid and
selecting "Edit Dummy Sites".



Linking of the input and output atoms

Structure Tidy output will give details about the original sequence number. This tab can be used to link
both input and output atoms (Fig. 16). Note that this process can sometimes be error-prone due to the
complexity of input/output, atom names, text truncation, etc. ...


Fig. 16: It is possible to link input and output atom names.


K-Plot processed entries

For entries that have been processed by K-Plot, a warning text will be displayed along with the input
data in order to indicate that the input data is different from the original ICSD entry. Pointing the mouse
to the text will display another balloon that further explains the change (Fig. 17).


Fig. 17: K-Plot processed files are displayed with a special warning, because they might be different from the original ICSD
entry.

Tidy Patch

Structure Tidy has some limitations on the atom type name and the number of unique element names.
Tidy Patch was created to avoid possible confusion.

When the user runs the Structure Tidy program by clicking the Update Standardization button, the
interface will try to create input text based on the contents on the input panel. Some modifications to
the original atom names, sequences, and dummy site representations may occur. There are three main
types of modifications:

1. If the atom name is longer than 2 letters or contains numbers, it will be replaced with dummy
labels in the input text, but the output grid displays will use the original names.
2. If there are more than 7 element names, all the element names will be replaced by a letter E
in the input text, but the output grids will use the original names (in this case, the dummy
definition line DEFINE QA will remain unchanged).
3. The sequence number in the input may not be used in creating the Structure Tidy input text;
new unique sequences will be created to make sure that all the sites have a unique
combination of element name and sequence number.

In general, if Tidy patch is used, there may not be a one-to-one correspondence between the input
text and the data on the input panel (if there is any modification on the atom label or sequence).
However, the data on the input panel should match with the data on the output panel display grids
(Standardized Entry and Link Atoms).

In order to match Structure Tidy input text with data on the input panel, Tidy patch has to be
disabled. To disable, go to Tools options, and check Disable Tidy Patch. Alternatively, you can
paste input text into the Read Input Text tab, and run Structure Tidy by clicking the Update and Run
button. The input will be fed into Structure Tidy without any modification.

Options

You may choose

how long the program can wait for
Structure Tidy to finish processing
whether or not to enable Tidy
patch
content of the print/save text.

(Fig. 18)



Fig. 18: Options of the ICSD Standardization tool.


The prerequisites for FindIt 2011-2 installation

These two prerequisites are for the Tidy application only, the user may ignore them if they do not need
to run the Tidy application. For users running win-2000 or earlier versions of windows system, they may
have to ignore these two prerequisites because the OS does not support them.

InstallShield will check the users computer for the two prerequisites; if either is missing, it will ask for
user permission to install it.

The .net framework package may require internet access to download files to finish installation.
The second prerequisite file (AccessDatabaseEngine.exe from MS) is included in the FindIt installation
package; InstallShield will simply run the local disk file to do the installation.

Both prerequisites are available online. The user can choose to download and install them manually
before running FindIt installation:

1. .net framework: Microsoft .NET Framework 3.5 Service Pack 1
(http://www.microsoft.com/download/en/details.aspx?id=22) requires WinXP or later version
OS.
2. ACE.OLEDB driver: 2007 Office System Driver: Data Connectivity Components
(http://www.microsoft.com/downloads/en/details.aspx?familyid=7554f536-8c28-4598-9b72-
ef94e038c891&displaylang=en) requires WinXP or later version OS.

The .net framework package may take a long time to install.

After prerequisite installation(s) is(are) done, InstallShield will resume the normal installation
procedure and continue the process.