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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 ...