chain.pdb. bio3d 2.3-0

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.

Description

Find possible chain breaks based on connective Calpha atom separation.

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 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.

Examples


# 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"

Author

Barry Grant

Find Possible PDB Chain Breaks