On Jul 13, 2012, at 4:00 PM, Christian Roth wrote:
> 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?
If you use UCSF Chimera (www.cgl.ucsf.edu/chimera), you can use the MatchMaker
tool to superimpose the structures. MatchMaker allows you to adjust the weight
of sequence similarity vs. secondary structure matching, so you can just make
the sequence similarity 0% and the secondary structure 100%. With the
structures superimposed, you can use the Match->Align tool to generate a
sequence alignment based solely on the proximity of residues to one another in
space. Be warned that Match->Align will be very slow for 10+ structures, but
is fine for half a dozen or so. The generated alignment will be displayed in a
window that will have a "File" menu where you can save the alignment to a
variety of common formats.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
