Working with CIFs

Well-known problem which concerns CIFs is the merging of data using the SHELX XCIF program when it resolves only question marks and leaves initialised values unchanged. Another problem is that the refinement cycle rewrites the CIF. To tackle these problems the CifX command is added to XFolders.

The command allows merging and extracting valuable information form CIFs as well as the creation of Summary Data Sheets using predefined RTF or HTML template.

Merging is necessary after the creation of CIF. If you create the CIF for the first time, it is better to create DS file (external file containing CIF data and used by the XFolders) with all option checked. This can be done from the "Save CIF Data to DS File" tab of the "CIF Data Tools" dialog. Checking all options allows collecting all possible information and the replacement of some tag values with default values (these can be edited from the "Preferences" dialog). The process happens like that: specified tags are extracted from CIF, merged with PCF values and later with Defaults. By this point some still unresolved or incorrect values (such as hkl limits or number of total reflections) values should be updated manually in the DS file. After this is done the "Merge" procedure can be used to update the CIF. The procedure automatically formats CIF.

The "Loop" tab provides some tolls to modify loops and to create ENVI-like tables from a CIF. To edit a loop simply double-click on corresponding item in the list or select an item ad press the "Edit" button. Use the "Make Table" button to create "Smart Table" - a ENVI-like table combining bond lengths and angles as shown below:

Bond lengths (Ǻ) and angles (˚) for the Ag1 environment observed in AG4PYY for: Ag1

	Ag1	N12'¹	N12²	N1'
N12'¹	2.222(4)	-
N12²	2.287(4)	118.58(16)	-
N1'	2.349(4)	131.68(13)	102.56(15)	-
N1	2.385(4)	112.15(15)	112.29(16)	69.52(15)
	¹: -x+y, -x, z ²: x-y, x, -z

	Simply check the items for which you want to create tables. Use "Select All", "Unselect All" and "Invert" commands to perform corresponding actions.
View of the "Smart Table" dialog

	The values of shown in the table can be edited manually or the "Replace Cif Data" dialog can be used to perform identical replacements. For example if a publication flag is needed to be set to "yes" for all items of the loop then it can be easily done using the dialog - simply specify what to find and what to replace.
View of the "Loop Edit" dialog.

View of the "Replace Cif Data" dialog.