Hello chimera friends: I am trying to get a structure-based sequence alignment for a pair of homologous proteins that are homodimers. If I proceed as described in the tutorial and in the 2006 BMC Bioinformatics paper, by first using Matchmaker, then using Match -> align, the Match -> Align fails to produce a reasonable alignment. The sequence identity from the Matchmaker output is 26.5%, but only 1.0 % from the Match -> Align step. If I delete the second monomer from each protein, Match -> Align works quite well. However, it seems like this alignment won't take into account any differences in the tertiary structure between the two proteins. That is, I think I want the global alignment of the whole dimer for the structural alignment, since the active sites is are at the interface. Any suggestions? I'm using version 1.2540, and my two proteins are PDB codes 1ds7 and 1nox (1nox dimer built from BIOMT matrix in Chimera and hand-edited to be 1 model with A and B chains). Thanks yet again, Eric