Biological Units Construction

Usage

biounit(pdb, biomat = NULL, multi = FALSE, ncore = NULL)

Arguments

pdb
an object of class pdb as obtained from function read.pdb.
biomat
a list object as returned by read.pdb (pdb$remark$biomat), containing matrices for symmetry operation on individual chains to build biological units. It will override the matrices stored in pdb.
multi
logical, if TRUE the biological unit is returned as a 'multi-model' pdb object with each symmetric copy a distinct structural 'MODEL'. Otherwise, all copies are represented as separated chains.
ncore
number of CPU cores used to do the calculation. By default (ncore=NULL), use all available CPU cores.

Value

a list of pdb objects with each representing an individual biological unit.

Description

Construct biological assemblies/units based on a 'pdb' object.

Details

A valid structural/simulation study should be performed on the biological unit of a protein system. For example, the alpha2-beta2 tetramer form of hemoglobin. However, canonical PDB files usually contain the asymmetric unit of the crystal cell, which can be:

  1. One biological unit
  2. A portion of a biological unit
  3. Multiple biological units

The function performs symmetry operations to the coordinates based on the transformation matrices stored in a 'pdb' object returned by read.pdb, and returns biological units stored as a list of pdb objects.

Examples


   # PDB server connection required - testing excluded

   pdb <- read.pdb("2dn1")



  Note: Accessing on-line PDB file



   biounit <- biounit(pdb)
   pdb




 Call:  read.pdb(file = "2dn1")

   Total Models#: 1
     Total Atoms#: 2506,  XYZs#: 7518  Chains#: 2  (values: A B)

     Protein Atoms#: 2172  (residues/Calpha atoms#: 285)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 334  (residues: 236)
     Non-protein/nucleic resid values: [ HEM (2), HOH (230), MBN (2), OXY (2) ]

   Protein sequence:
      LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKK
      VADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAV
      HASLDKFLASVSTVLTSKYRHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRF
      FESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFA...<cut>...HKYH

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



   biounit



$`AUTHOR.determined.tetramer (4 chains)`

 Call:  biounit(pdb = pdb)

   Total Models#: 1
     Total Atoms#: 5012,  XYZs#: 15036  Chains#: 4  (values: A B C D)

     Protein Atoms#: 4344  (residues/Calpha atoms#: 570)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 668  (residues: 472)
     Non-protein/nucleic resid values: [ HEM (4), HOH (460), MBN (4), OXY (4) ]

   Protein sequence:
      LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKK
      VADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAV
      HASLDKFLASVSTVLTSKYRHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRF
      FESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFA...<cut>...HKYH

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





   biounit <- biounit(read.pdb("2bfu"), multi=TRUE)



  Note: Accessing on-line PDB file



   write.pdb(biounit[[1]], file="biounit.pdb")
   # open the pdb file in VMD to have a look on the biological unit

See also

read.pdb

Author

Xin-Qiu Yao