Dear Chimera developers, I have a question related to the ³match² command. I wanted to align 4 related proteins and I used the default in the match menu. The alignment is fine; but I have a question about the output in the reply log. In the log it says: ³evaluating superpositions across all 439 fully populated columns in the final alignment² Then the pair-wise RMSD between the different pairs (range from 0.7 1.6 A) are given. What is meant by 439 fully populated columns? Does it mean 439 C-alpha atoms for those amino acids in the fully occupied aligned columns? I¹m asking because I want to report these values of RMSD and I want to be more specific and state the number of atoms over which the RMSD value is being reported. P.S. The proteins vary in their length (461,462,460 and 470). Thanks for your reply in advance, Ibrahim