On 13/07/12 15:30, Christian Roth wrote:
Dear all,
I want align a couple or protein structures by secondary structure matching to
one target and want get a kind of aminoacid alignment file e.g. what residue fit
the other, without adjustments due to sequence based alignments.
I tried Strap, but as far as I understood it, it takes also the sequence into
account. I tried also Rapido, but this does only a pairwise comparison.
Superpose does align it nicely (ccp4 based or Coot based) but there seems to
be no option to print the sequence alignment in a file and it is again just a
pairwise comparison .
It is not clear to me what you mean by "just" a pairwise comparison.
Coot outputs the SSM residue alignment to the terminal.
HTH,
Paul.
