Find Possible PDB Chain Breaks

Find possible chain breaks based on connective Calpha or peptide bond (C-N) atom separation.

chain.pdb(pdb, ca.dist = 4, bond=TRUE, bond.dist=1.5, 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.
bond	logical, if TRUE inspect peptide bond (C-N) instead of Calpha-Calpha distances.
bond.dist	cutoff value for C-N distance separation.
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 or peptide bond (C-N) atoms separated by at least bond.dist.

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.

References

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

Author

Barry Grant

See also

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

Examples

# \donttest{
# 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)
#> 	 Found 1 possible chain breaks
#> 	  After resno(s): 20 
#> 	  Chain length(s): 11, 4 
#>   [1] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A"
#>  [19] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A"
#>  [37] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A"
#>  [55] "A" "A" "A" "A" "A" "A" "A" "A" "A" "B" "B" "B" "B" "B" "B" "B" "B" "B"
#>  [73] "B" "B" "B" "B" "B" "B" "B" "B" "B" "B" "B" "B" "B" "B" "B" "B" "B" "B"
#>  [91] "B" "B" "B" "B" "B" "B" "B" "B" "B" "B"
# }