R: Write CRD File

write.crd {bio3d} | R Documentation

## 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.

### 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.

### Value

Called for its effect.

### Note

Check that `resno` and `eleno` do not exceed “9999”.

### Author(s)

Barry Grant

### 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

    ## Not run:
    # 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")

    ## End(Not run)

[Package bio3d version 2.3-4 Index]