bio3d (version 2.3-4)

chain.pdb: 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.

Value

Prints basic chain information and if rtn.vec 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.

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.

References

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

See Also

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

Examples

# NOT RUN {
# PDB server connection required - testing excluded

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)
# }