pdbfit(...)"pdbfit"(pdb, inds = NULL, ...)"pdbfit"(pdbs, inds = NULL, outpath = NULL, ...)
"pdb", as
obtained from read.pdb. "pdbs" containing PDB file
data, as obtained from read.fasta.pdb or
pdbaln. pdbfit.pdbs, and to
all calpha atoms for function pdbfit.pdb. fit.xyz function. Protein Databank Bank file coordinate superposition with the Kabsch algorithm.
The function pdbfit is a wrapper for the function
fit.xyz, wherein full details of the superposition procedure
are documented.
Input to pdbfit.pdbs should be a list object obtained with the
function read.fasta.pdb or pdbaln. See
the examples below.
For function pdbfit.pdb the input should be a multi-model
pdb object with multiple (>1) frames in the ‘xyz’
component.
The reference frame for supperposition (i.e. the fixed structure to
which others are superposed) is the first entry in the input
"pdbs" object. For finer control use fit.xyz.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
Kabsch Acta Cryst (1978) A34, 827--828.
#files <- get.pdb(c("4q21","5p21"), URLonly=TRUE) files <- get.pdb(c("4q21","5p21"), path=tempdir(), overwrite=TRUE) pdbs <- pdbaln(files)Reading PDB files: /tmp/RtmpTDihxb/4q21.pdb /tmp/RtmpTDihxb/5p21.pdb .. Extracting sequences pdb/seq: 1 name: /tmp/RtmpTDihxb/4q21.pdb pdb/seq: 2 name: /tmp/RtmpTDihxb/5p21.pdbxyz <- pdbfit(pdbs) # Superpose again this time outputing all-atom PDBs to disc #xyz <- pdbfit( pdbs, outpath="fitted" )