Ellipsoid plots are generated in the standard way [25] and [30]: a

unit sphere is scaled by the moduli of the eigenvalues in the three primary directions, rotated into the principal axis frame of the tensor and translated to the point of the corresponding nucleus. Blue axes are drawn inside for positive eigenvalues and red axes for negative eigenvalues. Dipolar interaction tensors are not visualized – inter-nuclear Idelalisib dipolar coupling is visually apparent from the distances and electron–nuclear dipolar coupling is contained in the hyperfine interaction. In systems with multiple electrons, the inter-electron dipolar coupling is either contained in the distances (in the individual electron spin representation) or in the zero-field splitting tensor (in the total electron spin representation). It is often the case in Magnetic Resonance simulations that electrons do not have specific Cartesian coordinates, being instead delocalized over the nuclear ensemble and manifesting themselves through hyperfine interactions. For this reason electrons are drawn separately Selleck Trametinib in the lower part of the central area of Fig. 3. Electron interaction ellipsoids rotate synchronously with the rest of the molecule, but the electrons themselves (visualized as translucent blobs)

do not move around the visualization window. Zero-field splitting tensors and g-tensors are visualized as ellipsoids centered on their corresponding electrons and inter-electron exchange couplings are shown as coils with the amplitude Vorinostat mouse mapped to the color. A summary of the visualization methods is given in Table 1. Visualization tab in the upper part of the main window controls the appearance and scaling of the ellipsoids as well as magnitude-color maps in the 3D view using logarithmic sliders. Visualization of individual interactions may be switched on and off using the tick boxes. NMR and EPR buttons switch the 3D view to the visualization of the corresponding interactions – shielding, shift, J-coupling,

quadrupolar coupling for the NMR mode; g-tensor, hyperfine coupling, exchange coupling, zero-field splitting for the EPR mode. The primary format for spin system data storage and retrieval is SpinXML, but the GUI can also import Gaussian 03/09 logs (*.log, *.out), Cartesian XYZ files (*.xyz, coordinates only, isotopes are guessed) and both versions of CASTEP files (*.magres). When multiple instances of the relevant tables are present in the file (e.g. multiple coordinate sections in geometry optimizations), the last section is read. For Gaussian 03/09 calculations, the detailed printing option is required in the route section of the input file. Electronic structure theory calculations often produce large quantities of small interactions (e.g.