Crystallography tools menu (left-bottom)

 Show lattice vectors       This menu item shows the crystal cell parameters (a, b, c, alpha, beta, gamma):

Show crystal cell                The same

Show asymmetric unit             Shows the atoms printed in the .cif file here:

Show unit cell content (wrapped coordinates)  

This is the default display mode. The coordinates from the asymmetric unit are translated according to all transformations written in the "_symmetry_equiv_pos_as_xyz" section. After the coordinates translation, some of the atoms can overlap:

Overlapped atoms are cut by Chemcraft by default. In tools/preferences, you can alter the default distance threshold for cutting.

Note that the fractional coordinates from the previous point are wrapped, i.e. only their fractional parts are taken (e.g. 1.15 becomes 0.15, -0.25 becomes 0.75, etc):

Show symmetry equivalent positions (non-wrapped coordinates) Does the same but does not wrap the coordinates. Note that if the molecule produced by this menu item contains overlapping atoms (with same coordinates), you can remove them via "Edit/Operations with atomic coordinates/Cut overlapping atoms" in the main menu;

Show duplicated cell    The crystal cell can be unlimitedly duplicated in different directions:

Note that with the subitems of this menu item, you cap specify any size of the duplicated molecule, or the duplicated molecule with non-integer boundaries;

Show labels on atoms      With this menu item, you can show the numbers of atoms in the default cell for a duplicated molecule;

Show structural parameters from the file     

Some .cif files contain structural parameters (bond lengths, angles, dihedrals, etc). These parameters must be already computed by the programs which generates .cif files. Because in crystallography the position of an atom is not a precise point, but instead a smudge of electron density, spread over a (typically) non-spherical area, these parameters are more accurate, than the parameters, calculated by Chemcraft by the Cartesian coordinates of atoms:

Show structural subunit extracted from 5*5*5 duplicated cell by selected atoms 

This tool can be a convenient addition to other tools for investigating what atoms are in a specific part of the molecule. It does the same as if you duplicate the cell to 5*5*5 size, then select a file and choose Tools/Fragments extractor menu item in the main window;

Increase the distance cutoff so there will be no overlapping atoms (closer than 0.3 Angs)

If your cif file produces overlapping atoms, choose this menu item. Note that the threshold of 0.3 Angs can be altered via "Tools/Preferences/.cif files/Atom distance threshold for manual cutting";

Wrap fractional coordinates    Wraps the coordinates with two possible approaches;

Convert the atomic coordinates     The coordinates of atoms in molecule will be recomputed to fractional ones or vice versa (this is not convenient for visualization, but you can switch to Coord menu and see the values of the fractional coordinate);

Calculate bonds by short contacts (VDW radii)  Computes the bonds in molecule by Van-Der-Waals radii;

Redefine lattice       This menu item allows you to rebuild the crystal, describing new A, B, C vectors in terms of old;

Build slab         This menu item builds a slab (Miller index) useful for investigating a surface of a crystal (e.g. for heterogeneous catalysis );

Rebuild cif file by current molecule     If you have made any modifications of the molecule's structure on the image in the main windows, you need to use this menu item before saving cif/vasp file (this menu item updates the data stored in the hierarchical list at left-top, which is used for e.g. building duplicated cells);

Recompute cell ABC parameters from lattice vectors     Some output files contain only the lattice vectors instead of the cell parameter (a, b, etc), and in some programs (Quantum Espresso), the lattice vectors can be presented in an orientation which is considered as non-standard by Chemcraft (e.g. A.y is nonzero). In this case, you need to reorient your molecule before saving a .cif file;

Show/edit crystal cell parameters    You can use this menu item for altering e.g. the length of the C vector in your crystal;

Save .cif or vasp file     Saves current crystal data (stored in the hierarchical list at left-top) to a file (also see above about the "Recompute cell ABC parameters" menu item);

Notes:

If Chemcraft incorrectly identifies bonds in molecule, you should use the "Tools/Chemcraft incorrectly identifies..." menu item or manually set all bonds via Ctrl+B. To make a bond dotted, double-click on it and alter its type (make it "H-bond").

If you work with CIF files, we recommend checking them via CheckCIF:

http://checkcif.iucr.org/

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