Radius of Gyration

Usage

rgyr(xyz, mass=NULL, ncore=1, nseg.scale=1)

Arguments

xyz
a numeric vector, matrix or list object with an xyz component, containing one or more coordinate sets.
mass
a numeric vector of atomic masses (unit a.m.u.), or a PDB object with masses stored in the "B-factor" column. If mass==NULL, all atoms are assumed carbon.
ncore
number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
nseg.scale
split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.

Description

Calculate the radius of gyration of coordinate sets.

Details

Radius of gyration is a standard measure of overall structural change of macromolecules.

Value

Returns a numeric vector of radius of gyration.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples

# PDB server connection required - testing excluded # -- Calculate Rog of single structure pdb <- read.pdb("1bg2")
Note: Accessing on-line PDB file
mass <- rep(12, length(pdb$xyz)/3) mass[substr(pdb$atom[,"elety"], 1, 1) == "N"] <- 14 mass[substr(pdb$atom[,"elety"], 1, 1) == "H"] <- 1 mass[substr(pdb$atom[,"elety"], 1, 1) == "O"] <- 16 mass[substr(pdb$atom[,"elety"], 1, 1) == "S"] <- 32 rgyr(pdb, mass)
[1] 19.8667
# -- Calculate Rog of a trajectory xyz <- read.dcd(system.file("examples/hivp.dcd", package="bio3d"))
NATOM = 198 NFRAME= 117 ISTART= 0 last = 117 nstep = 117 nfile = 117 NSAVE = 1 NDEGF = 0 version 24 Reading (x100) |======================================================================| 100%
rg <- rgyr(xyz) rg[1:10]
[1] 17.50097 17.38617 17.45981 17.40144 17.32908 17.37739 17.46936 17.62601 [9] 17.45649 17.47451

See also

fit.xyz, rmsd, read.pdb, read.fasta.pdb

Author

Xin-Qiu Yao & Pete Kekenes-Huskey