chain.pdb {bio3d} | R Documentation |
Find possible chain breaks based on connective Calpha atom separation.
chain.pdb(pdb, ca.dist = 4, blank = "X", rtn.vec = TRUE)
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. |
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.
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.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
read.pdb
, atom.select
, trim.pdb
,
write.pdb
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)