RemoveOoR.b: Remove B-value Out of Range Atoms

In vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins

Description

Removes atoms with B-values out of accepted range.

Usage

RemoveOoR.b(atoms.chains.oi)

Arguments

atoms.chains.oi

The data.frame containing the PDB file information; aka the PDB structure

Details

Accepted B-value values range from 0 to 100 with values. Atoms are considered stationary – possessing low thermal energy – when possessing values between 20 and 40 while larger values between 60 and 100 indicate a large amount of position variability within the lattice. This function identifies occupancy values less than 0 and greater than 100 and removes them from the structure.

Value

data.frame of the PDB structure without the offending atoms

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

Other "Clean Protein Structure": CleanProteinStructures, RemoveHydrogenAtoms, RemoveModeledAtoms, RemoveOoR.o, RetainWatersWithinX

Examples

  
  nrow(PDB.4ape$atom)
  PDB.4ape.OoR.b <- RemoveOoR.b(PDB.4ape$atom)
  nrow(PDB.4ape.OoR.b)
  

vanddraabe documentation built on June 8, 2019, 1:03 a.m.