CVs Documentation

The following list contains descriptions of a number of the colvars that are currently implemented in the PLUMED-ISDB module. These collective variables are related to the definitions of models to interpret experimental observables. They can be used in combination with any other collective variable, function or bias also outside the ISDB module.

 CS2BACKBONE Calculates the backbone chemical shifts for a protein. EMMI Calculate the fit of a structure or ensemble of structures with a cryo-EM density map. FRET Calculates the FRET efficiency between a pair of atoms.The efficiency is calculated using the Forster relation: JCOUPLING Calculates $$^3J$$ coupling constants for a dihedral angle. NOE Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms or ambiguous NOE. PCS Calculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization. PRE Calculates the Paramagnetic Resonance Enhancement intensity ratio between a spin label atom and a list of atoms . RDC Calculates the (Residual) Dipolar Coupling between two atoms. SAXS Calculates SAXS scattered intensity using either the Debye equation.