bio3d (version 2.4-4)

biounit: Biological Units Construction

Description

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

Usage

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

Value

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

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.

Author

Xin-Qiu Yao

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.

See Also

read.pdb

Examples

# \donttest{
   # PDB server connection required - testing excluded

   pdb <- read.pdb("2dn1")
   biounit <- biounit(pdb)
   pdb
   biounit
# }
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
}