Hi - SSM algorithm at PDBeFold will do this sort of thing
http://www.ebi.ac.uk/msd-srv/ssm/ I wrote a tutorial for multiple alignment to go with a Phaser story http://www.ebi.ac.uk/pdbe-apps/quips?story=Phaser&auxpage=MultiplePDBeFoldminitutorial The last page of this tells you where to get an multiple fastA alignment of the superimposed structures and explains the format. Hope that helps. Martyn Martyn Symmons EBI Cambridge ________________________________ From: Eric Pettersen <p...@cgl.ucsf.edu> To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, 16 July 2012, 2:17 Subject: Re: [ccp4bb] strict structure based alignment 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
