chain.pdb {bio3d}R Documentation

Find Possible PDB Chain Breaks

Description

Find possible chain breaks based on connective Calpha atom separation.

Usage

chain.pdb(pdb, ca.dist = 4, blank = "X", rtn.vec = TRUE)

Arguments

pdb a PDB structure object obtained from read.pdb.
ca.dist the maximum distance that separates Calpha atoms considered to be in the same chain.
blank a character to assign non-protein atoms.
rtn.vec logical, if TRUE then the one-letter chain vector consisting of the 26 upper-case letters of the Roman alphabet is returned.

Details

This is a basic function for finding possible chain breaks in PDB structure files, i.e. connective Calpha atoms that are further than ca.dist apart.

Value

Prints basic chain information and if ca.dist is TRUE returns a character vector of chain ids consisting of the 26 upper-case letters of the Roman alphabet plus possible blank entries for non-protein atoms.

Author(s)

Barry Grant

References

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

See Also

read.pdb, atom.select, trim.pdb, write.pdb

Examples

full.pdb <- read.pdb( get.pdb("5p21", URLonly=TRUE) )
inds <- atom.select(full.pdb, resno=c(10:20,30:33))
cut.pdb <- trim.pdb(full.pdb, inds)
chain.pdb(cut.pdb)

[Package bio3d version 1.0-6 Index]