Write CRD 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.

Description

Write a CHARMM CARD (CRD) coordinate file.

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.

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.

Note

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

Examples

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



  Note: Accessing on-line PDB file



summary(pdb)




 Call:  read.pdb(file = "1bg2")

   Total Models#: 1
     Total Atoms#: 2733,  XYZs#: 8199  Chains#: 1  (values: A)

     Protein Atoms#: 2527  (residues/Calpha atoms#: 323)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 206  (residues: 174)
     Non-protein/nucleic resid values: [ ACT (3), ADP (1), HOH (169), MG (1) ]

+ attr: atom, xyz, seqres, helix, sheet,
        calpha, remark, call



# Convert to CHARMM format
new <- convert.pdb(pdb, type="charmm")



	 Retaining 2733 non-hydrogen atoms
	 Converting to 'charmm' format
	 Non-standard residue names present ( MG ACT ADP HOH )
	 Found 0 possible chain breaks



summary(new)




 Call:  read.pdb(file = "1bg2")

   Total Models#: 1
     Total Atoms#: 2733,  XYZs#: 8199  Chains#: 1  (values: NA)

     Protein Atoms#: 2527  (residues/Calpha atoms#: 323)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 206  (residues: 174)
     Non-protein/nucleic resid values: [ ACT (3), ADP (1), HOH (169), MG (1) ]

+ attr: atom, xyz, seqres, helix, sheet,
        calpha, remark, call



# Write a CRD file
write.crd(new, file="4charmm.crd")

See also

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

Author

Barry Grant