Graphical Interface for the Crystal Structures

To know where to begin, make sure you have read the tutorials first ! Crystal.jpg

3D Crystal view

3D Crystal view: Fourier maps

Crystal Menus

Crystal Options

Crystal Unit Cell & Spacegroup

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: 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:

Crystal Scatterers

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

Atom

Atom.jpg

Z-Scatterer(molecule, polyhedron)

Molecule (organic compound, inorganic polyhedron)

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:

Starting in Fox 1.8.1, a Molecule can generate new random configurations using Molecular dynamics (MD) principles. This is useful for molecules where the conformation cannot be changed solely by rotation around free torsions, e.g. molecules with large flexible cycles. To control these moves there are two parameters available:

None: Manual/Crystal (last edited 2009-03-28 23:24:46 by VincentFavreNicolin)