bio3d (version 2.1-3)

dssp.trj: Secondary Structure Analysis of Trajectories with DSSP

Description

Secondary structure assignment according to the method of Kabsch and Sander.

Usage

dssp.trj(pdb, trj, skip=1000, threshold=3, file.head="")

Arguments

pdb

a structure object of class "pdb", obtained from read.pdb.

trj

a trajectory object of class "trj", obtained from read.ncdf, read.dcd, read.crd.

skip

a number indicating the frame frequency in the trajectory indicated; default = 1000.

threshold

a number indicating the threshold to be used for the analysis: higher numbers will decrease the threshold, allowing to accept structures with smaller secondary structure differences, with respect of the reference pdb structure; default = 3

file.head

a path where to save the structures with possible unfolding events.

Value

• This function gives, as output, a comparative secondary structure analysis between different structures: particularly, the frame number under analysis will be printed on screen if the structure shows possible unfolding events and the frame structure will be saved, according with the file.head indicated.

Details

This function calls the DSSP program and calculates the secondary structure difference between the reference pdb and frames from the trj file indicated, according with the skip value indicated.

References

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

DSSP is the work of Kabsch and Sander: Kabsch and Sander (1983) Biopolymers. 12, 2577--2637.

For information on obtaining DSSP, see: http://swift.cmbi.ru.nl/gv/dssp/.

See Also

read.pdb, read.ncdf, read.dcd, read.crd, plot.bio3d, dssp

Examples

# Read a PDB file
pdb <- read.pdb(system.file("examples/hivp.pdb", package="bio3d"))
trj <- read.dcd(system.file("examples/hivp.dcd", package="bio3d"))

dssp.trj(pdb, trj, skip = 100, threshold = 1.5)