vanddraabe (version 1.1.1)

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

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

Value

data.frame of the PDB structure without the offending atoms

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.

See Also

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

Examples

# NOT RUN {
  
# }
# NOT RUN {
  nrow(PDB.4ape$atom)
  PDB.4ape.OoR.b <- RemoveOoR.b(PDB.4ape$atom)
  nrow(PDB.4ape.OoR.b)
  
# }
# NOT RUN {
# }