Dear Christian,
PDBefold superimposes the structures and generates the sequence
alignment in fasta(??) format. You can then read this file in Multialign
for example to get the sequence alignment and then add the secondary
structures to the sequence alignment using ESPript for example.
David
On 07/13/2012 04:30 PM, 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 .
> Is there an other program which does something similar?
>
> Best Regards
>
> Christian
>
--
David Cobessi
Institut de Biologie Structurale
41, Rue Jules Horowitz
38027 Grenoble Cedex-1, France
Tel:33(0)438789613
33(0)608164340
Fax:33(0)438785122
