write.pdb. bio3d 2.3-0

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, sse = FALSE,  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.
sse: logical, if TRUE secondary structure annotations are written.
print.segid: logical, if FALSE segid will not be written.

Description

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

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.

Value

Called for its effect.

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.

Note

Check that: (1) chain is one character long e.g. “A”, and (2) resno and eleno do not exceed “9999”.

Examples


# PDB server connection required - testing excluded

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

  Note: Accessing on-line PDB file


# 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") )


See the output file:
/tmp/RtmpTDihxb/eg.pdb

Author

Barry Grant with contributions from Joao Martins.

Write PDB Format Coordinate File