O -- the manual

Manual for O version 5.10

T.A Jones ¶ & Morten Kjeldgaard §

The figure above shows a bit of helix A with density from elongation factor EF-Tu-GDPNP from Thermus aquaticus (Kjeldgaard, M. et al. (1993) Structure, 1, 35--50). The plot was generated with O and converted to POSTSCRIPT with oplot.

• Contents
• Preface
• Introduction
  • General description
  • Hardware requirements
  • Basic design
  • The O database
  • Menus
  • The command line interpreter
  • Objects
  • Getting help...
  • What to do about Bugs
• Operation
  • Workstation versions
  • Getting started...
  • SGI 4D extensions
  • Dials
• 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
• An O Tutorial.
  • Example 1: Getting started with a set of coordinates
  • Example 2: Colouring the molecule
  • Example 3: Using skeletons
  • Example 4: Customizing the screen menu
• How to ...
  • How to Colour atoms
  • How to Change the values in a datablock
  • How to Read in external data from own programs
  • How to move a map file from a VAX to a workstation
  • How do I get my skeleton to my workstation?
  • How do I build a complete molecule from a set of CA atoms?
  • How to rescue a corrupted database?
• Crystallographic model building
• General Drawing Instructions
  • The syntax of the O graphics descriptor language
  • Using the Draw_object command
• Associated programs
  • bones
  • mappage
  • Brix --- yet another map paging program...
  • The averaging programs --- A
  • mkcol
  • dispcol
  • oplot
    • The oplot output
    • Hints for plotting with O
    • The oplot input
    • Viewing instructions
    • Example
    • Some tricks
    • Compiling oplot
    • Known bugs & limitations
• References
• TERMS OF AGREEMENT
• Workstation Distribution of O
  • ESV specific installation
  • Running the Program.
• Sorted Required Datablocks
• Examples of Residue Tables
• Distributed Macros
  • @bones_20a
  • @bones_50a
  • @change_id_colour
  • @change_id_colour
  • @change_id_number
  • @Save_as
  • @map
  • @paint_by_atom_type
  • @paint_by_b_factor
  • @paint_by_internal_residue
  • @sphere
  • @two_molecules
  • Menu systems included
• The Refi Dictionary
• Index
• About this document ...

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