clean.pdb. bio3d 2.3-0

Usage

clean.pdb(pdb, consecutive = TRUE, force.renumber = FALSE, fix.chain = FALSE, fix.aa = FALSE, rm.wat = FALSE, rm.lig = FALSE, rm.h = FALSE, verbose = FALSE)

Arguments

pdb: an object of class pdb as obtained from function read.pdb.
consecutive: logical, if TRUE renumbering will result in consecutive residue numbers spanning all chains. Otherwise new residue numbers will begin at 1 for each chain.
force.renumber: logical, if TRUE atom and residue records are renumbered even if no 'insert' code is found in the pdb object.
fix.chain: logical, if TRUE chains are relabeled based on chain breaks detected.
fix.aa: logical, if TRUE non-standard amino acid names are converted into equivalent standard names.
rm.wat: logical, if TRUE water atoms are removed.
rm.lig: logical, if TRUE ligand atoms are removed.
rm.h: logical, if TRUE hydrogen atoms are removed.
verbose: logical, if TRUE details of the conversion process are printed.

Value

a 'pdb' object with an additional $log component storing all the processing messages.

Description

Inspect alternative coordinates, chain breaks, bad residue numbering, non-standard/unknow amino acids, etc. Return a 'clean' pdb object with fixed residue numbering and optionally relabeled chain IDs, corrected amino acid names, removed water, ligand, or hydrogen atoms. All changes are recorded in a log in the returned object.

Details

call for its effects.

Examples


   # PDB server connection required - testing excluded

   pdb <- read.pdb("1a7l")

  Note: Accessing on-line PDB file

   clean.pdb(pdb)


 Call:  clean.pdb(pdb = pdb)

   Total Models#: 1
     Total Atoms#: 8750,  XYZs#: 26250  Chains#: 3  (values: A B C)

     Protein Atoms#: 8634  (residues/Calpha atoms#: 1114)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 116  (residues: 51)
     Non-protein/nucleic resid values: [ HOH (48), MAL (3) ]

   Protein sequence:
      EGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWA
      HDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLP
      NPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGV
      DNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTING...<cut>...KDGS

+ attr: atom, xyz, seqres, helix, sheet,
        calpha, remark, call, log

Author

Xin-Qiu Yao & Barry Grant

Inspect And Clean Up A PDB Object