TableOfContents(4)

1. Graphical Interface for the Crystal Structures

To know where to begin, make sure you have read the [:FoxTutorials: tutorials first !] attachment:Crystal.jpg

1.1. 3D Crystal view

1.2. Crystal Menus

1.3. Crystal Options

1.4. Crystal Unit Cell & Spacegroup

1.5. Crystal Scattering Powers (atom types)

To access the Scattering Powers parameters, you can use the Crystal "Scatterers->Show Scattering Powers Parameters Window" menu, which opens the window: attachment:ScatteringPower.jpg In the opened window there are 3 tabs available. In the first one you can define the Following parameters:

Note about AntiBump and BondValence cost functions:

1.6. Crystal Scatterers

The Scatterers in each Crystal structure can be either individual atoms or molecules (including polyhedra).

1.6.1. Atom

attachment:Atom.jpg

1.6.2. Z-Scatterer(molecule, polyhedron)

1.6.3. Molecule (organic compound, inorganic polyhedron)

attachment:Molecule.jpg

A Molecule is defined by a list of atoms with their xyz coordinates (in an orthonormal reference frame internal to the molecule), with the geometry of the Molecule set by a list of restraints: bond lengths, bond angles, dihedral angles and rigid groups of atoms. The orientation of the Molecule is defined internally by a quaternion, so the orientation parameters are not directly accessible.

Usually a Molecule (the atoms and the restraints defining its geometry) is automatically created by importing a z-matrix. But if you want to manually create a Molecule, first use the Scatterer menu of the Crystal to create a Molecule, and then using the menus of the Molecule Object, add all the atoms, and then all the restraints (bond lengths, angles, dihedral angles).

A few notes when creating Molecules:

To see the list of bonds, bond angles, dihedral angles and rigid groups you can use the menu "Formula->Show Restraint Window":

Notes about restraints:

There are three options for a Molecule: