| TOP command | Python equivalent |
| ADD_RESTRAINT | Restraints.add() |
| ALIGN | alignment.align() |
| ALIGN2D | alignment.align2d() |
| ALIGN3D | alignment.align3d() |
| ALIGN_CONSENSUS | alignment.consensus() |
| ALN_TO_PROF | alignment.to_profile() |
| BUILD_MODEL | model.build() |
| BUILD_PROFILE | profile.build() |
| CALL | use Python subroutines |
| CHECK_ALIGNMENT | alignment.check() |
| CLOSE | use Python file object |
| COLOR_ALN_MODEL | model.color() |
| COMPARE | alignment.compare_structures() |
| COMPARE_ALIGNMENTS | alignment.compare_with() |
| CONDENSE_RESTRAINTS | Restraints.condense() |
| DEBUG_FUNCTION | selection.debug_function() |
| DEFINE_INTEGER | use Python 'int' variables |
| DEFINE_LOGICAL | use Python 'bool' variables |
| DEFINE_REAL | use Python 'float' variables |
| DEFINE_STRING | use Python 'str' variables |
| DEFINE_SYMMETRY | Restraints.add() |
| DELETE_ALIGNMENT | del(alignment) |
| DELETE_FILE | modfile.delete() |
| DELETE_RESTRAINT | Restraints.unpick() |
| DENDROGRAM | environ.dendrogram() |
| DESCRIBE | alignment.describe() |
| DO | use Python while or for loops |
| EDIT_ALIGNMENT | alignment.edit() |
| EM_GRID_SEARCH | density.grid_search() |
| END_SUBROUTINE | use Python subroutines |
| ENERGY | selection.energy() |
| EXIT | use Python while or for loops |
| EXPAND_ALIGNMENT | use alignment.append_model() in a loop |
| GENERATE_TOPOLOGY | model.generate_topology() |
| ID_TABLE | alignment.id_table() |
| IF | use Python if statement |
| INCLUDE | use Python import statement |
| INQUIRE | modfile.inquire() |
| IUPAC_MODEL | model.to_iupac() |
| MAKE_CHAINS | model.make_chains() |
| MAKE_REGION | model.make_region() |
| MAKE_RESTRAINTS | Restraints.make() |
| MAKE_SCHEDULE | schedule.make_for_model() |
| MAKE_TOPOLOGY_MODEL | Topology.make() |
| MALIGN | alignment.malign() |
| MALIGN3D | alignment.malign3d() |
| MUTATE_MODEL | selection.mutate() |
| OPEN | use Python file object |
| OPERATE | use Python arithmetic |
| OPTIMIZE | conjugate_gradients() or molecular_dynamics(), or <schedule> objects |
| ORIENT_MODEL | model.orient() |
| PATCH | model.patch() |
| PATCH_SS_MODEL | model.patch_ss() |
| PATCH_SS_TEMPLATES | model.patch_ss_templates() |
| PICK_ATOMS | Use <selection> objects |
| PICK_HOT_ATOMS | selection.hot_atoms() |
| PICK_RESTRAINTS | Restraints.pick() |
| PRINCIPAL_COMPONENTS | environ.principal_components() |
| PROFILE_PROFILE_SCAN | profile.scan() |
| PROF_TO_ALN | alignment.append_profile() or profile.to_alignment() |
| RANDOMIZE_XYZ | selection.randomize_xyz() |
| READ | use Python file object |
| READ_ALIGNMENT | alignment.append() |
| READ_ALIGNMENT2 | alignment.append() |
| READ_ATOM_CLASSES | group_restraints() |
| READ_DENSITY | density.read() |
| READ_MODEL | model.read() |
| READ_MODEL2 | model.read() |
| READ_PARAMETERS | Parameters.read() or group_restraints.append() |
| READ_PROFILE | profile.read() |
| READ_RESTRAINTS | Restraints.append() |
| READ_RESTYP_LIB | environ() |
| READ_SCHEDULE | Use <schedule> objects |
| READ_SEQUENCE_DB | sequence_db.read() |
| READ_TOPOLOGY | Topology.read() or Topology.append() |
| REINDEX_RESTRAINTS | Restraints.reindex() |
| RENAME_SEGMENTS | model.rename_segments() |
| REORDER_ATOMS | model.reorder_atoms() |
| RESET | do not use |
| RETURN | use Python subroutines |
| ROTATE_DIHEDRALS | selection.rotate_dihedrals() |
| ROTATE_MODEL | selection.translate(), selection.transform(), or selection.rotate_origin() |
| SALIGN | alignment.salign() |
| SEGMENT_MATCHING | alignment.segment_matching() |
| SEQFILTER | sequence_db.filter() |
| SEQUENCE_COMPARISON | alignment.compare_sequences() |
| SEQUENCE_SEARCH | sequence_db.search() |
| SEQUENCE_TO_ALI | alignment.append_model() |
| SET | use Python variables |
| SPLINE_RESTRAINTS | Restraints.spline() |
| STOP | do not use |
| STRING_IF | use Python if statement |
| STRING_OPERATE | use Python arithmetic |
| SUBROUTINE | use Python subroutines |
| SUPERPOSE | selection.superpose() |
| SWITCH_TRACE | actions.trace() |
| SYSTEM | environ.system() |
| TIME_MARK | info.time_mark() |
| TRANSFER_RES_NUMB | model.res_num_from() |
| TRANSFER_XYZ | model.transfer_xyz() |
| UNBUILD_MODEL | selection.unbuild() |
| WRITE | use Python file object |
| WRITE_ALIGNMENT | alignment.write() |
| WRITE_DATA | model.write_data() |
| WRITE_MODEL | model.write() |
| WRITE_MODEL2 | model.write() |
| WRITE_PDB_XREF | use <residue> objects |
| WRITE_PROFILE | profile.write() |
| WRITE_RESTRAINTS | Restraints.write() |
| WRITE_SCHEDULE | schedule.write() |
| WRITE_SEQUENCE_DB | sequence_db.write() |
| WRITE_TOP | do not use |
| WRITE_TOPOLOGY_MODEL | Topology.write() |
| TOP variable | Python equivalent |
| ALIGN_CODES | Sequence.code |
| ATOM_FILES | Sequence.atom_file |
| ATOM_FILES_DIRECTORY | io_data.atom_files_directory |
| CONTACT_SHELL | energy_data.contact_shell |
| COULOMB_SWITCH | energy_data.coulomb_switch |
| COVALENT_CYS | energy_data.covalent_cys |
| DYNAMIC_ACCESS | do not use |
| DYNAMIC_COULOMB | energy_data.dynamic_coulomb |
| DYNAMIC_LENNARD | energy_data.dynamic_lennard |
| DYNAMIC_MODELLER | energy_data.dynamic_modeller |
| DYNAMIC_PAIRS | set automatically; do not use |
| DYNAMIC_SPHERE | energy_data.dynamic_sphere |
| EXCL_LOCAL | energy_data.excl_local |
| HETATM_IO | io_data.hetatm |
| HYDROGEN_IO | io_data.hydrogen |
| LENNARD_JONES_SWITCH | energy_data.lennard_jones_switch |
| MOLPDF | return value from selection.energy() |
| NLOGN_USE | energy_data.nlogn_use |
| NONBONDED_SEL_ATOMS | energy_data.nonbonded_sel_atoms |
| NUMB_OF_SEQUENCES | len(alignment) |
| N_SCHEDULE | len(schedule) |
| OUTPUT_CONTROL | use log.level() |
| RADII_FACTOR | energy_data.radii_factor |
| RELATIVE_DIELECTRIC | energy_data.relative_dielectric |
| SCHEDULE_STEP | do not use |
| SPHERE_STDV | energy_data.sphere_stdv |
| TOPOLOGY_MODEL | Topology.submodel |
| UPDATE_DYNAMIC | energy_data.update_dynamic |
| WATER_IO | io_data.water |