Hi, I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details: Model 1 is to be aligned to Model 2; each model only has one chain Model 1 positions (residues=amino acids) 11-323 Model 2 positions ( residues=amino acids) 24-336 When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms. Here is what I thought would work: align #1:11-323 to_atoms #2:24-336 Here is the error message: Unequal number of atoms to pair, 2483 to 2371 I am still trying to understand the nomenclature for understanding residues and atoms. Thanks for any help you can provide. Phil McClean