Good Morning to everyone, it’s my first time here writing at you, I hope I’m doing right. The point is that I’m working with a wild type enzyme from which I got mutant versions by using swap aa command. My goal is to look at the effects that mutations have on the structure by superimposing the mutant form with the wild type one. When I perform matchmaker command, RMSD is equal to 0 and the structures overlap perfectly; thus I thought to minimize structure before superimposing and in this way I see a little difference in RMSD but it could be due to the different steps of the minimize process (e.g. adding protons) than the actual effect of mutations. Moreover when I perform multiple sequence alignment, the amminoacids I swapped actually are not different from the Wild type ones. If I point the cursor on the swapped aa I see the difference in name and side chain but by doing multiple sequence alignment they do not appear. Any suggestions? Inviato da Posta<https://go.microsoft.com/fwlink/?LinkId=550986> per Windows 10