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
.
The more advanced (and also more useful) effect is giving complete mappings
from the column indices of the original alignment (aln$ali
) to
atomic indices of equivalent C-alpha atoms in the pdb
. These mappings
are stored in the output list (see below 'Value' section). This feature
is better illustrated in the function pdb2aln.ind
, which
calls pdb2aln
and directly returns atom selections given a set of
alignment positions. (See pdb2aln.ind
for details. )
When aln.id
is provided, the function will do pairwise alignment
between the sequence from pdb
and the sequence in aln
with id matching aln.id
. This is the best way to use the
function if the protein has an identical or very similar sequence
to one of the sequences in aln
.