vanddraabe (version 1.1.1)

RemoveModeledAtoms: Remove Modeled Atoms

Description

Removes modeled atoms from a RCSB/PDB structure.

Usage

RemoveModeledAtoms(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 modeled atoms

Details

Sometimes atoms are not well resolved within the electron density maps and the scientists resolving/determining the structures "model back into" the resulting structure the atoms based on historical data. This is most common for residues where a portion of the residue is missing and based on the structure the missing atoms are replaces. These modeled atoms have an occupancy value of 0.01 or less and are identified and removed.

The reported occupancy value of 0.01 is used as the cutoff because several PDB structures have comments in the REMARK 3 section stating, "...MISSING ABOVE 1SIGMA WERE GIVEN A 0.01 OCCUPANCY..."`` or "...WITH NO DENSITIES ARE GIVEN OCCUPANCY VALUES OF 0.01..."`.

See Also

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

Examples

# NOT RUN {
  
# }
# NOT RUN {
  PDB.1ecd.noModeledAtoms <- RemoveModeledAtoms(PDB.1ecd$atom)
  
# }
# NOT RUN {
# }