Chemcraft Gallery - tools for crystallographers

Chemcraft reads .cif, Crystal, Quantum Espresso, Shellx, Vasp and other files, and saves .cif and Vasp files with crystallorgaphy data. A set of tools is provided for convenient analysis and processing of the data from crystallography files:

1. Chemcraft can be used for visualizing .cif files and building slabs (Miller indices):

2. Crystallographers can also find the Fragments Extractor useful:

3. When .cif files are visualized, the distance cutoff can be increased, so there will be no overlapping atoms (with distance less than e.g. 0.5 A). Use the "Crystallography tools/Increase the distance cutoff..." menu item at left-bottom:

4. Besides the standard cell duplication option, Chemcraft has a "Fragments extractor" tool: you can select some atoms in the crystal, and the program will "expand" them for showing neighboring atoms (atoms which are bonded to these selected atoms). This is a convenient way to visualize individual molecules (connected groups of atoms) in a crystal. This tool is activated via "Crystallography tools/Show structural subunit extracted from 5*5*5..." menu item. At the picture below, all atoms in 1*1*1 cell were selected and then "expanded" in the Fragments extractor tool, so you can see all molecules in this crystal:

5. When a crystal contains several molecules, it can be convenient to enumerate all of them. To do this, you should firstly select all atoms via "Edit/Select all" menu item in the main window, then choose "Crystallography tools/Show structural subunit extracted from 5*5*5..." at the left, then choose "Tools/Show molecules if any atoms in them..." in the Fragments Extractor window, then press "Close and apply...", and then choose "Tools/Divide current structure..." in the main window:

6. Sometimes a crystal is a single big molecule, but the cells are connected through specific atoms types. e.g. metal atoms; in this case, it can be convenient to set the option to block atoms expanding for these specific atom types in the Fragments Extractor. This picture was obtained after expanding the atoms to maximum with this limitation:

7. The "Fragments extractor" tool can do atoms expanding not only by the bonding information, but also simply by distances between atoms - for example you can select some atoms and the program will add to them the atoms which are closer to them than e.g. 4 angstroms. This tool can be useful for quick understanding of specific regions of interests (defects. pores):

Back.