Biological Units Construction

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

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.

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.

Author

Xin-Qiu Yao

See also

read.pdb

Examples

# \donttest{
   # 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
#> 
# }
if (FALSE) {
   biounit <- biounit(read.pdb("2bfu"), multi=TRUE)
   write.pdb(biounit[[1]], file="biounit.pdb")
   # open the pdb file in VMD to have a look on the biological unit
}