bio3d (version 2.1-3)

write.crd: Write CRD File

Description

Write a CHARMM CARD (CRD) coordinate file.

Usage

write.crd(pdb = NULL, xyz = pdb$xyz, resno = NULL, resid = NULL, 
   eleno = NULL, elety = NULL, segid = NULL, resno2 = NULL, b = NULL, 
   verbose = FALSE, file = "R.crd")

Arguments

pdb

a structure object obtained from read.pdb or read.crd.

xyz

Cartesian coordinates as a vector or 3xN matrix.

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.

segid

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

resno2

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

b

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

verbose

logical, if TRUE progress details are printed.

file

the output file name.

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 segid and B-factors equal to 0.00.

References

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

For a description of CHARMM CARD (CRD) format see: http://www.charmmtutorial.org/index.php/CHARMM:The_Basics.

See Also

read.crd, read.pdb, atom.select, write.pdb, read.dcd, read.fasta.pdb, read.fasta

Examples

# Read a PDB file
pdb <- read.pdb( "1bg2" )
summary(pdb)
# Convert to CHARMM format
new <- convert.pdb(pdb, type="charmm")
summary(new)
# Write a CRD file
write.crd(new, file="4charmm.crd")