General Procedure
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The first step is to enter or import the data for the crystal to be transformed. To import from one of several file formats, choose Import from the File menu. After selecting the format, you will see the Import File dialog. The 3-letter file extension ".xxx" in the edit box will be used to filter the files (that is, the Open File dialog will show only the files with this extension). Any changes you make in file extensions will be saved for future runs. Some formats may offer a choice of symmetry option; if the file actually lists symmetry "as XYZ", that is in the form of the positions of the general equipoint for the space group in the International Tables for X-ray Crystallography.

To enter the data manually, choose New from the File menu.

In the first dialog which appears, Title/Axes, supply an 80-character title, and specify the unit-cell parameters.

The two Symmetry options are Space Group and Custom. The Space Group option lists almost all standard orientations and origins, so this is usually the first choice. You can type in a Hermann-Maughin or Hall symbol, or give the International Tables number, but it is normally safest to select the space group in the scrolling list and double-click on it or click the Select button (be sure the symbols/number for the selected group appears in the edit boxes above). If you type in the H-M symbol, it is interpreted either according to Volume I of the 1952 edition of the International Tables , or Volume A of the 1983 edition. The main difference between the two is that in Volume I the default orientation for monoclinic crystals is a-axis unique, and in Volume A the default is b-axis unique. That is, if you type in "P2/m" the orientation will be different. Of course to be certain you can also type in the long form "P112/m" or "P12/m1", or select one of these in the list.

If the space group is a non-standard one, such as C-1 (Cbar1), it will be necessary to use the Custom Symmetry option. Often you can start with the Space Group option and then switch to the Custom option (Change Symmetry Option button) and make modifications as necessary. In the list of operations you must supply (if they are not there already), the coordinates of the equivalent positions of the general equipoint as listed in the International Tables , one per line. If the space group is centrosymmetric and the origin is on a center of inversion, select the Centric radio button and supply only half the operations – the center will be supplied by CRYSCON. If the origin is not on a center of inversion, you must supply all the operations and select the Acentric radio button.

In the Input Atom (Site) dialog, supply the standard atomic parameters. The type is normally the atomic number, but it could also be an arbitrary number. If there is only one occupant of the site or position it is not necessary to enter the data in the list box. If there is multiple occupancy, click on Add and supply the parameters as necessary in the Atom Sharing a Site dialog. For a cell/symmetry tranformation such multiple occupancies are seldom used - they are simply carried over for possible Export. The label and type of the main entry will be those of the first occupant.

When the atom list is complete you are done with the "Old" crystal. The atom list is shown in the Control Window. You can save this file or document at any time with the Save or SaveAs options in the File menu.

General Procedure for Cell/Symmetry Tranformation

Now click on the Transform button to specify the parameters of the "New" crystal. In the Tranformation Parameters dialog, click on the Symmetry button if the symmetry of the New crystal is to be different from the old symmetry. Specify the symmetry as above. The symmetry specified here pertains to the New orientation, not the Old. The default symmetry is the same as the Old.

Three types of transformation can be carried out - Translation only, Input atoms only, and Full unit cells. Input atoms only is the only option which will transform anisotropic temperature factors and/or atomic vectors (magnetic, displacement, etc.). See Tranformation Parameters for more details.

The parameters specified in the Tranformation Parameters dialog, going downward in the dialog, correspond to the operations successively carried out by CRYSCON.

First, translations may be applied to the input atom coordinates (Pre-symmetry translations). If the origin for your atom coordinates does not correspond to that of the standard symmetry specified for the Old crystal, corrections must be made here. If you select Translation only , this is all that will be done – the remainder of the parameters are ignored.

Input atoms only option:

CRYSCON applies the Pre-matrix translations, transforms the coordinates of the Old input atoms only, and applies the Post-matrix translations. (Pre-symmetry translations are not used). This gives a set of input atoms for the New structure, and the tranformation is complete. Anisotropic temperature factors and atomic vectors are transformed to the new unit cell.

Full unit cells option:

CRYSCON now generates all the atoms in the Old unit cell. If the origin of the New unit cell differs from that of the Old, with respect to the common symmetry elements, you must make corrections in the Pre-matrix translations edit boxes. Such differences among sub/supergroups are common, and it may be necessary to study the diagrams and coordinates in the International Tables to get these translations.

CRYSCON now transforms the coordinates according to the matrix supplied. Now it has the contents of the Old unit cell, expressed in coordinates of the New unit cell.

In order to fill out the contents of a supercell, or to shift the contents for a reorientation, CRYSCON now systematically adds and subtracts the New unit-cell vectors.

Next, in order to average atom positions for a subcell or an increase in symmetry, CRYSCON similarly adds and subtracts the Old unit-cell vectors. If the position of a new atom generated in this way falls within the specified distance, or Tolerance, the atomic positions are averaged. CRYSCON keeps a running count of the number of atoms averaged in this way. The tolerance should be large enough to avoid having quasi-superimposed atoms in the result, but of course it must be less than the smallest bond length in the structure. Setting this may take some trial and error. A value of 0.4-0.5 seems to be large enough for even rather extreme cases of atomic shifts in sub/supercells and sub/supergroups.

Post-matrix translations may be applied here if the standard origin for the New space group is different from that of the Old space group. This is an alternative to the Pre-matrix translations - it should not be necessary to use both.

At this point, there should be a complete and hopefully realistic set of atoms for the New unit cell. Depending on the symmetry change, the new set may or may not conform to the New symmetry. CRYSCON now applies the New symmetry to eliminate symmetry-equivalent atoms. Again a tolerance is applied to decide if atom positions are "coincident". This generates a standard set of symmetry-unique atoms, or the "asymmetric unit". However, in many cases when generating a subcell or increasing the symmetry the averaging process does not put the new atoms exactly on special symmetry positions.

CRYSCON now applies the new symmetry to the supposed asymmetric unit, to generate a complete set of atoms for the New unit cell. You should know, based on simple volume considerations, how many total atoms are expected in the New unit cell. If the number of atoms in the unit cell generated in this step does not agree with that generated by transformation (before symmetry consolidation), CRYSCON now prints out the number it has generated and asks if you want to recycle to refine the location of atoms on special positions. If the atoms in special positions were not located within tolerance (.0001??) in the previous step, extra atoms will be generated, and the total generated will be greater than expected. If so, "recycling" will repeat the previous step of reducing to the asymmetric unit, and hopefully averaging will place the atom positions closer to the symmetry elements, if not on them (within tolerance). It may take several cycles of no change in number before the number of atoms generated comes down to the number expected. If there appears to be no improvement after 3 or 4 cycles, inspection of the results is in order - the correction to the atoms in special positions may be obvious, or it may appear that the matrix and/or translations are not valid.

When you decline another cycle, the process is terminated and the results appear in a special Output Text or Edit window (see Types of Windows). This window has a separate menu bar, with standard entries for text editing. This text document or output file can be saved separately from the input data (which is in files with extension .cco) using the Save and SaveAs option in this menu bar.

Note that when different input atoms are consolidated during a transformation, for example super- to sub-cell or on increasing the symmetry, CRYSCON does not attempt to combine the two sets of occupancies; it simply takes the list of occupants from the first atom generated.

In the Full unit cells option, CRYSCON does not attempt to transform anisotropic temperature factors; if there are anisotropic temperature factors they are converted to isotropic B's in the New structure. Atomic vectors are not transformed either - the New atoms will have vectors which are simply copied from the first Old input atom which was used to generate the New atom.

To go back to the main data input, click on the Control Window or use the Window menu to switch. The process or tranformation can be repeated without removing the Output window, but its contents will be replaced. If you want to save successive results files, use the SaveAs option (when the Ouput file is active or has the focus) to give the file a different name (eg myfile1.ccd) before recalculating.

The transformed (New) input atoms (symmetry-unique atoms) can be converted into the original (Old) input atoms with the Transformed to Input option in the Input menu.

Other Operations

There are several things which can be done without Transformation. All these operations may be done on the transformed atoms, as well as the original atoms, after a transformation has been carried out.

Bond Lengths and Angles. The Bond Lengths and Angles button in the Control Window will call up a special dialog for this.

Powder and Precession diffraction simulation. See the Powder Diffraction and Precession Pattern dialogs.

Exporting Files. You can write files containing either the Old data or the New data in most of the same format as are available for import. Select Export in the File menu. In the case of input files for structure refinement programs, such as SHELX, RIETAN, DBWS/LHPM, etc. CRYSCON cannot supply all of the required parameters, only the symmetry, unit cell and atomic positions and temperature factors. Non-essential information such as comments is also not necessarily passed on, but in most cases the relevant lines can simply be copied from the import file (Old crystal) to the export file (New Crystal).