Extract sequence from a PDB object and align it to an existing multiple sequence alignment that you wish keep intact.

pdb2aln(aln, pdb, id="seq.pdb", aln.id=NULL, file="pdb2aln.fa", ...)

## Arguments

aln an alignment list object with id and ali components, similar to that generated by read.fasta, read.fasta.pdb, and seqaln. the PDB object to be added to aln. name for the PDB sequence in the generated new alignment. id of the sequence in aln that is close to the sequence from pdb. output file name for writing the generated new alignment. additional arguments passed to seqaln.

## Details

The basic effect of this function is to add a PDB sequence to an existing alignement. In this case, the function is simply a wrapper of seq2aln.

## References

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

## Author

Xin-Qiu Yao & Barry Grant

seqaln, seq2aln, seqaln.pair, pdb2aln.ind

## Examples

if (FALSE) {
##--- Read aligned PDB coordinates (CA only)