bio3d (version 2.1-2)

write.pdb: Write PDB Format Coordinate File

Description

Write a Protein Data Bank (PDB) file for a given xyz Cartesian coordinate vector or matrix.

Usage

write.pdb(pdb = NULL, file = "R.pdb", xyz = pdb$xyz, type = NULL, resno = NULL,
 resid = NULL, eleno = NULL, elety = NULL, chain = NULL, insert = NULL, 
 alt = NULL, o = NULL, b = NULL, segid = NULL, elesy = NULL, charge = NULL, 
append = FALSE, verbose = FALSE, chainter = FALSE, end = TRUE, print.segid = FALSE)

Arguments

pdb

a PDB structure object obtained from read.pdb.

file

the output file name.

xyz

Cartesian coordinates as a vector or 3xN matrix.

type

vector of record types, i.e. "ATOM" or "HETATM", with length equal to length(xyz)/3.

resno

vector of residue numbers of length equal to length(xyz)/3.

resid

vector of residue types/ids of length equal to length(xyz)/3.

eleno

vector of element/atom numbers of length equal to length(xyz)/3.

elety

vector of element/atom types of length equal to length(xyz)/3.

chain

vector of chain identifiers with length equal to length(xyz)/3.

insert

vector of insertion code with length equal to length(xyz)/3.

alt

vector of alternate record with length equal to length(xyz)/3.

o

vector of occupancy values of length equal to length(xyz)/3.

b

vector of B-factors of length equal to length(xyz)/3.

segid

vector of segment id of length equal to length(xyz)/3.

elesy

vector of element symbol of length equal to length(xyz)/3.

charge

vector of atomic charge of length equal to length(xyz)/3.

append

logical, if TRUE output is appended to the bottom of an existing file (used primarly for writing multi-model files).

verbose

logical, if TRUE progress details are printed.

chainter

logical, if TRUE a TER line is inserted at termination of a chain.

end

logical, if TRUE END line is written.

print.segid

logical, if FALSE segid will not be written.

Value

• Called for its effect.

Details

Only the xyz argument is strictly required. Other arguments assume a default poly-ALA C-alpha structure with a blank chain id, occupancy values of 1.00 and B-factors equal to 0.00. If the input argument xyz is a matrix then each row is assumed to be a different structure/frame to be written to a multimodel PDB file, with frames separated by END records.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. For a description of PDB format (version3.3) see: http://www.wwpdb.org/documentation/format33/v3.3.html.

See Also

read.pdb, read.dcd, read.fasta.pdb, read.fasta

Examples

# Read a PDB file
pdb <- read.pdb( "1bg2" )

# Renumber residues
nums <- as.numeric(pdb$atom[,"resno"])
nums <- nums - (nums[1] - 1)

# Write out renumbered PDB file
outfile = file.path(tempdir(), "eg.pdb")
write.pdb(pdb=pdb, resno = nums, file = outfile)

invisible( cat("\nSee the output file:", outfile, sep = "\n") )