Description of Commands

• Menus
• The Draw_Mol commands
  • Object_name
  • Molecule_name
  • Ca_zone
  • Zone
  • Cover_sphere
  • Sphere_centre
  • End_object
  • Delete_object
  • Connect_file
  • Examples
  • Customizing the message and atom labels
  • Macros
  • Datablocks
• The Paint commands
  • Paint_property
  • Paint_ramp
  • Paint_case
  • Paint_zone
  • Paint_select
  • Paint_object
  • Paint_obj_zone
  • Paint_obj_atom
  • Paint_colour
  • Personalized Colours
• The Notes menu
  • Note_setup
  • Note_name
  • Note_object
  • Note_id_add
  • Note_xyz_add
  • Note_sphere
• The Sketch commands
  • Sketch_setup
  • Sketch_object
  • Sketch_type
  • Sketch_add
  • Sketch_undo
  • Sketch_auto
  • Sketch_stick
  • Sketch_cpk
  • Example
  • A note on solid surfaces
• The Select commands
  • Select_on
  • Select_off
  • Select_property
  • Select_visible
  • Select_invert
  • Examples
• The Manip menu
  • Move_atom
  • Move_zone
  • Move_fragment
  • Flip_peptide
  • Move_object
  • Tor_residue
  • Tor_general
  • Examples
  • Datablocks used by the Manip menus
• The Trig commands
  • Dist_define
  • Trig_reset
  • Trig_refresh
  • Neighbour_atom
  • Neighbour_residue
  • Hbonds_mc
  • Hbonds_all
  • Phi_Psi
  • Angle_define
  • Example
  • Datablock used
• The LSQ commands
  • Lsq_explicit
  • Lsq_improve
  • Lsq_object
  • Lsq_molecule
  • Lsq_paired_atoms
  • Examples
  • Macros
  • Datablocks for the LSQ menu
• The Map commands
  • Map_File
  • Map_object
  • Map_param
  • Map_Atom_Centre
  • Map_Active_Centre
  • Map_Xyz_Centre
  • Map_info
  • Map_draw
  • Map_Cache
  • Map_cover
  • Examples
  • Datablocks for the Map menus
• The Quick Map commands
  • Qm_setup
  • Qm_file
  • Qm_draw
  • Qm_zap
• The Bones commands
  • Bone_setup
  • Bone_draw
  • Bone_redefine
  • Bone_Ca_Id
  • Bone_repeat
  • Bone_skip
  • Bone_break_bond
  • Bone_make_bond
  • Bone_mask
  • Bone_Ca_zone
  • Examples
  • Macros
• The Lego commands
  • Lego_setup
  • Lego_Ca
  • Lego_bones
  • Lego_Auto_MC
  • Lego_Side_Chain
  • Lego_Auto_SC
  • Lego_Loop
• The RSR commands
  • RSR_setup
  • RSR_map
  • RSR_scale
  • RSR_zone
  • RSR_rigid
  • RSR_rotamer
  • RSR_dgnl
  • RSR_contours
  • The RSR dictionary
• The Refi commands
  • Refi_setup
  • Refi_zone
  • Datablocks for the Refi Option
• The Sam commands
  • Sam_atom_in
  • Sam_atom_out
  • Sam_list_sequ
  • Sam_init_db
  • Water_init
  • Water_add
  • Water_pekpik
  • Merge_atoms
  • Sam_rename
  • Datablocks
• The Assorted_1 commands
  • Centre_ID
  • Terminal_ID
  • Wait_ID
  • Stop
  • Yes
  • No
  • Clear_flags
  • Save_DB
  • Clear_Id
  • Macros
  • Datablocks
• The Assorted_2 commands
  • Menu_control
  • Symbols
  • O_setup
  • Help
  • Spawn
  • $
  • Stereo
  • Rot_Tran_Obj
  • Macros
• The Assorted_3 commands
  • Centre_atom
  • Centre_XYZ
  • Backup_DB
  • Message
  • Draw_object
  • Dial_next
  • Dial_previous
  • Dial_box
  • Rotate_picture
  • Cpk_object
  • Screen_colour
  • Spin
  • Print
  • Bell
  • If_yes_no
  • Centre_zone
  • Centre_next
  • Centre_prev
  • Quit
• The O_heap_1 commands
  • Directory
  • Db_create
  • Db_delete
  • Read_formatted
  • Write_formatted
  • Db_table_residue
  • Db_set_data
  • Db_set_zone
  • Db_set_atom
  • A smart-ass example
• The O_heap_2 commands
  • Rot_trans_Db
  • Arith_Db
  • Copy_Db
  • Db_kill
  • DB_stat
• The special major menus Object_1 to 5
  • On_off
• The Symmetry commands
  • Symm_setup
  • Symm_sphere
  • Symm_object
  • Symm_cell
  • Examples
  • Datablocks
• The Plot commands
  • Plot_setup
  • Plot
  • Plot_on
  • Plot_off
• Patterson
  • Patt_setup
  • Patt_cross
  • Patt_move
• Mutate
  • Mutate_setup
  • Mutate_replace
  • Mutate_delete
  • Mutate_insert
  • Example: menu_mutate.o
• Slider
  • Slider_setup
  • Slider_guess
  • Slider_show
  • Slider_display
  • Slider_combine
  • Slider_lego
  • Datablocks Used
• Utilities
  • Pep_flip
  • RS_fit
  • YASSPA
  • RSC_fit
  • EZD_map
  • EZD_draw
• Mask Commands
  • Mask_setup
  • Mask_read
  • Mask_write
  • Mask_off
  • Mask_on
  • Mask_contour
  • Mask_object
  • Examples
  • Datablocks
• MolRep -- Molecular Replacement
  • MR_setup
  • MR_rt
• Trace Commands
  • Baton_build
  • Baton_mode
  • Trace_setup
  • Trace_prune
  • Trace_fill_Ca
  • Bone_prune
  • Bone_excise
  • Bone_branch
  • Bone_undo