Normal Mode Analysis

This logic performs a Normal Mode Analysisof the given 3d structure. It can be used to visualize basic molecular movement modes.

The logic has three modes that represent the three different major parts of NMA. In the first step the volume is filled with pseudo atoms. In the second step an elastic network is created with respect to the positions of the pseudo atoms. It is based on a Hessian Matrix and a cutoff distance. Last, eigenvector/eigenvalue decomposition is performed and in a last step they are applied on the pseudoatoms. The workflow is split into 3 separate parts to allow the user to check intermediate results.

Choose between the three different NMA-steps Fit Pseudo Atoms Into Volume, Compute Normal Modes or Apply Normal Modes.

Fills the 3D volume with pseudo atoms. Two modes are accessible. Either Sphere Packing that is filling out the whole volume or Random placing pseudo atoms in a randomized manner into the model volume. The lower the number of pseudo atoms of the NMA-model, the less the computational expensiveness for further applications.

• Pseudoatom Radius: Radius of pseudoatoms in pixel. Should be 1.0 or more.
• Relative Pseudoatom Overlaps: Determines how much of a given volume must be covered by a pseudoatom. Fully covered == 1.0. Note that a value between [0,1] means that pseudoatoms can intersect.

NOTE: you can check the fitting result by double clicking the PseudoAtomVisualization IO. You can also check the number of pseudo atoms by clicking on the 3d once.