Hi, SSM (via PDBefold) (http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver) will do a structure based alignment and outputs a table of rmsd but will not give you a alignment file as such.
-Sujata On Fri, Jul 13, 2012 at 10:30 AM, Christian Roth < christian.r...@bbz.uni-leipzig.de> 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 >
