- sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
- sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
+ sb.append("select ").append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY)).append("|");
+ sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY)).append(getCommandSeparator())