pdbaln. bio3d 2.3-0

Usage

pdbaln(files, fit = FALSE, pqr = FALSE, ncore = 1, nseg.scale = 1,  ...)

Arguments

files: a character vector of PDB file names. Alternatively, a list of pdb objects can be provided.
fit: logical, if TRUE coordinate superposition is performed on the input structures.
pqr: logical, if TRUE the input structures are assumed to be in PQR format.
ncore: number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
nseg.scale: split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.
...: extra arguments passed to seqaln function.

Description

Create multiple sequences alignments from a list of PDB files returning aligned sequence and structure records.

Details

This wrapper function calls the underlying functions read.pdb, pdbseq, seqaln and read.fasta.pdb returning a list of class "pdbs" similar to that returned by read.fasta.pdb.

As these steps are often error prone it is recomended for most cases that the individual underlying functions are called in sequence with checks made on the valadity of their respective outputs to ensure sensible results.

Value

xyz: numeric matrix of aligned C-alpha coordinates.
resno: character matrix of aligned residue numbers.
b: numeric matrix of aligned B-factor values.
chain: character matrix of aligned chain identifiers.
id: character vector of PDB sequence/structure names.
ali: character matrix of aligned sequences.
call: the matched call.

References

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

Note

See recommendation in details section above.

Examples

##- Align PDBs (from vector of filenames)
#files <- get.pdb(c("4q21","5p21"), URLonly=TRUE)
files <- get.pdb(c("4q21","5p21"), path=tempdir(), overwrite=TRUE)
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.pdb 

                             1        .         .         .         .         50 
[Truncated_Name:1]4q21.pdb   MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGET
[Truncated_Name:2]5p21.pdb   MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGET
                             ************************************************** 
                             1        .         .         .         .         50 

                            51        .         .         .         .         100 
[Truncated_Name:1]4q21.pdb   CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQI
[Truncated_Name:2]5p21.pdb   CLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQI
                             ************************************************** 
                            51        .         .         .         .         100 

                           101        .         .         .         .         150 
[Truncated_Name:1]4q21.pdb   KRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQ
[Truncated_Name:2]5p21.pdb   KRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQ
                             ************************************************** 
                           101        .         .         .         .         150 

                           151        .       168 
[Truncated_Name:1]4q21.pdb   GVEDAFYTLVREIRQHKL
[Truncated_Name:2]5p21.pdb   GVEDAFYTLVREIRQH--
                             ****************   
                           151        .       168 

Call:
  pdbaln(files = files)

Class:
  pdbs, fasta

Alignment dimensions:
  2 sequence rows; 168 position columns (166 non-gap, 2 gap) 

+ attr: xyz, resno, b, chain, id, ali, resid, sse, call



##- Align PDBs (from list of existing PDB objects)
pdblist <- list(read.pdb(files[1]), read.pdb(files[2]))
pdbaln(pdblist)



Extracting sequences

pdb/seq: 1   name: seq1 
pdb/seq: 2   name: seq2 

       1        .         .         .         .         .         .         70 
seq1   MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQ
seq2   MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQ
       ********************************************************************** 
       1        .         .         .         .         .         .         70 

      71        .         .         .         .         .         .         140 
seq1   YMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIP
seq2   YMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIP
       ********************************************************************** 
      71        .         .         .         .         .         .         140 

     141        .         .       168 
seq1   YIETSAKTRQGVEDAFYTLVREIRQHKL
seq2   YIETSAKTRQGVEDAFYTLVREIRQH--
       **************************   
     141        .         .       168 

Call:
  pdbaln(files = pdblist)

Class:
  pdbs, fasta

Alignment dimensions:
  2 sequence rows; 168 position columns (166 non-gap, 2 gap) 

+ attr: xyz, resno, b, chain, id, ali, resid, sse, call

Author

Barry Grant

Sequence Alignment of PDB Files