Hi, as Jeff pointed out last week, using phenix.pdbtools you can be very selective in what you keep/remove. Just a few examples: - remove all waters: phenix.pdbtools model.pdb remove=water - remove all waters and DNA/RNA: phenix.pdbtools model.pdb remove="water or dna or rna" - remove all protein sidechains: phenix.pdbtools model.pdb remove="protein and sidechain" or equivalently: phenix.pdbtools model.pdb keep="all and not (protein and sidechain)" - keep only oxygens: phenix.pdbtools model.pdb keep="element O" - keep only nitrogens in protein sidechains: phenix.pdbtools model.pdb keep="protein and sidechain and element N" - keep only backbone in chain A and in chain C: phenix.pdbtools model.pdb keep="(chain A and backbone) or (chain C and backbone)" - remove residues in chain A from number 3 to 25: phenix.pdbtools model.pdb remove="chain A and resseq 3:25" ... and so on. To get more familiar with atom selection syntax you can practice by running the command phenix.pdb_atom_selection model.pdb ATOM_SELECTION_STRING for example: phenix.pdb_atom_selection model.pdb "chain A and resseq 1:100" which will output the selected atoms to the screen. Some examples of atom selection syntax can be found here: http://phenix-online.org/documentation/refinement.htm#anch88 Pavel.