|
|
|
| Home | Live Data | Instruments | CHRNS | Proposals |
The crystallographic information file, (CIF) was developed by the IUCr in the early 1990's as a standardized format to document single-crystal structure determinations and to exchange the results between laboratories. The data items used in CIF are described in a series of data dictionaries. The syntax used in these data dictionaries is described in a data definition language (DDL), of which there are two versions DDL 1.4 and DDL 2.1. The data dictionary for the original single-crystal information (now called the core) as well as the powder diffraction (pdCIF) dictionary use a somewhat updated version of the original syntax, DDL 1.4, while the macromolecular CIF (mmCIF) dictionary uses the more complex DDL 2.1.
The CIFEDIT program, described here, was created to view and edit CIFs, with particular emphasis on files that contain multiple blocks, as these are quite important in pdCIF. For DDL 1.4 version dictionaries, CIFEDIT can use information from the dictionaries to validate CIF data items, as well as display the definitions for these items.
Contents:
On Windows and Macintosh computers, CIFEDIT will usually be invoked by dragging a CIF onto the icon for CIFEDIT. Alternately, one can click on the icon and then locate the appropriate file via a file open window. One can also configure the operating system to associate a file extension (such as .CIF), so that double clicking (or in Windows left-clicking) on such a file will open that CIF in CIFEDIT. This configuration can be selected for Windows during installation. For Macintosh, the user must do this for themselves.The CIFEDIT program is started on Unix computers typically by typing
cifedit [file.cif]where optionally the name of a file, file.cif, to be read is listed on the command line. If no file is supplied on the command line, a file browser is opened to select a file to use.
While the CIF is being read, a message such as the one to the right will be seen. After the read is complete, the main CIFEDIT screen (shown below) displays the CIF data block(s) and data items in a hierarchical format.
The minus sign (-) to the left of block name data_NISI_publ can be toggled using the mouse to hide all of the data items included in the block, as is shown to the left.
As is shown to the left, the "folder" icon indicates a data block, a single page indicates a CIF data item and an icon with a pair of pages indicates a data loop. The contents of loops is not shown, by default, but clicking on the plus sign (+) to the left of the loop causes the entry to be expanded to show the contents. As an example, contrast the difference between loop_0, and loop_2 to the left.
As is shown above, clicking on a CIF data item causes the value associated with that data item to be displayed in the right-hand side window. In the example shown above, the data name _cell_length_a has been selected. This is defined in the CIF dictionary as a number between 0 and infinity with units of Angstroms. These units (A) are displayed adjacent to the entry box.
If the mode is changed from "browse" to "edit" (see control in lower right), the value can be edited, as is seen below. When appropriate, input is validated to require that valid numbers in the allowed range are input and that standard uncertainties (esd's) are entered only where allowed. Likewise, if the CIF dictionary defines a enumerated list of values for a data name, a menu button is offered in place of an entry box. In this way, only a valid entry from the list can be selected.
CIF loops
CIF loops allow multiple values to be associated with one or more data items, in effect defining a table of data. Clicking on the entry for a loop causes all the data names in the loop to be displayed, as is shown below.
When a loop is displayed, extra controls appear, as are defined below. Note that only the first entry listed will be available in "Browse" mode.It is also possible to click on the data name for a item inside a loop, in this case, all entries for that data item in the loop are displayed (a column). This mode is not available for very large loops, as it would require too much memory to display all the entries. The maximum number of entries is controlled by variable CIF(maxRows), which can be customized.
- Loop element #
- The Loop element #" spinbox" is used to select which "row" from the loop is displayed. The up arrow advances to the next row, while the down arrow reverses by one entry. Numbers can also be typed into the entry box; the number is accepted when Enter is pressed. The keyboard up and down arrows can also be used to advance between entries. Other keys such as Page Up, Home, etc. advance in large increments.
- Add to loop
- In edit mode, a new row can be added to the end of a loop using the "Add to loop" button. The value for each new entry is initialized as "?" (meaning value unknown or unspecified.)
- Delete loop entry
- In edit mode, this deletes the current row from the loop. First select the row to delete with the "Loop element #" spinbox. Note that the values are displayed for confirmation before the delete operation is performed. It is not possible to delete all entries from a loop, so this button is disabled when a loop has only a single row defined.
CIF errors
Parse Errors
If errors are noted as a CIF is parsed, a special entry is listed immediately after the block name, labeled "Parse-errors", as is shown below. Note that the "go to line" button in the Show (Hide) CIF contents window can be very convenient for locating and repairing these errors.
Validation Errors
Many other types of errors can be determined by comparing data values against the definitions found in the appropriate CIF dictionary. For example, the core dictionary specifies that the only valid names for _diffrn_radiation_probe are x-ray, neutron, electron, and gamma. If a CIF has this value specified as proton, it will be flagged as an error. Likewise, _atom_type_number_in_cell is specified as number, zero or greater. An error condition will exist, if the value for this is specified as a negative number, or a string than is not a valid number (the special CIF values . and ? are valid, however). Pressing the "Validate CIF" button at the bottom of the main window causes the CIF to be scanned for errors in data values. If errors are located, a window will be displayed. Also, a entry with "Validation-errors" is added to the browser.
As CIF data names are selected, their definitions are shown in the
CIF Definitions window, as shown to the right.
After the "Show CIF definitions" button is pressed, the label changes to
"Hide CIF definitions"; pressing the button again causes the
window to be hidden.
