9. biomacromolecules (bio)

9.1. MDA universe

MDAnalysis scatteringUniverse creation with additional methods for adding hydrogens, volume determination and merging of biological assemblies from PDB structures. See the MDAnalysis User Guide’s for non scattering topics.

9.2. Formfactors

Formfactors of universes containing a protein or DNA. Explicit hydration layer might be included allowing simultaneous SAXS/SANS fitting.

9.3. Effective diffusion of rigid structures

Effective diffusion D(Q) for scalar trans/rot or tensor diffusion coefficients.

9.4. Intermediate scattering functions (ISF)

The time dependent intermediate scattering function I(Q,t) describes changes in scattering intensity due to dynamic processes of an atomic structure.

9.5. Normal modes

arg61_animation

Normal modes of atomic structures using the Anisotropic Network Model (ANMA) implementing mass or friction weighted mode analysis.

  • See example in ANMA() for usage and how to deform structures.

  • See different NM for specific methods as raw(), rmsd(), animate(), allatommode(), forceConstant(), frequency(), effectiveMass(), effectiveFriction(), invRelaxTime(),