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O11 release notes

O12 release notes

O13 release notes

O14 release notes

New users

Updated 2017-01-16



O

Commands
A
Arcade_setup
ASA_display
Angle_define
Arith_db
AutO_2ry
AutO_build
B
Backup_DB
Bell_ring
Bond_break
Bond_make
Bone Overview
Bone_Ca_Id
Bone_Ca_zone
Bone_branch
Bone_draw
Bone_excise
Bone_mask
Bone_prune
Bone_redefine
Bone_repeat
Bone_sc_set
Bone_setup
Bone_skip
Bone_undo
Build commands
Build_altern(ate)
Build_ed_gro(up)
Build_ed_loo(p)
Build_ed_res(idue)
Build_ed_rot
Build_ed_to
Build_init
Build_molecu(le)
Build_nucleu(s)
Build_residu(e)
Build_rotome(r)
Build_slider
C
Ca_zone
Centre_atom
Centre_build
Centre_id
Centre_next
Centre_previous
Centre_xyz
Centre_zone
Clear_flags
Clear_id
Connect_code
Continue_no
Continue_yes
Copy_db
Cover_sphere
CPK_object
D
Db_and
Db_average
Db_a2r_average
Db_create
Db_delete
Db_kill
Db_or
Db_set_atom
Db_set_data
Db_set_group
Db_set_zone
Db_statistics
Db_table_residue
Decor overview
Decor_easy
Decor_fast
Decor_step_1
Decor_step_2
Decor_fix
Decor_free
Decor_guess
Decor_show
Decor_slider
Decor_yasspa
Delete_objec(t)
Dials in O
Dial_box
Dial_next
Dial_previous
Directory
Dist_define
Draw_object
E
End_object
Error_exit
EZD_draw
EZD_map
F
Flip_peptide
Fm Overview
Fm_draw
Fm_file
Fm_local_a(verage)
Fm_mode
Fm_multiply
Fm_rsr_grou(p)
Fm_rsr_rota(mer)
Fm_rsr_tors(ion)
Fm_rsr_zone
Fm_setup
Fm_zap
G
Gamepad (Linux)
Grab Overview
Grab_atom
Grab_build
Grab_fragment
Grab_group
Grab_guide
Grab_residue
H
Hbonds_all
Hbonds_mc
Help
HKL Overview
HKL_chop_F(ourier)
HKL_Fourier
HKL_read
HKL_SF_chop
HKL_SF_expli(cit)
HKL_SF_map
HKL_SF_model
HKL_upd_Fo(urier)
HKL_signal
I
If_Yes_No
J
Job_submit
Job_check
Job_reset
Job REFMAC
Job REFMAC chop
Job EDS fetch
L
Lego Overview
Lego_Auto_MC
Lego_Auto_SC
Lego_Bones
Lego_Ca
Lego_Loop
Lego_Setup
Lego_Side_Ch(ain)
Loop Overview
Loop_define
Loop_next
Loop_setup
Loop_text
Lsq Overview
Lsq_axis
Lsq_chain_op
Lsq_Explicit
Lsq_Improve
Lsq_Molecule
Lsq_Object
Lsq_Paired_A(toms)
Lsq_proper
M
Menu_control
Merge_atoms
Message
Molecule_nam(e)
Move_object
Move_zone
MR_rt
MR_setup
Mutate Overview
Mutate_1st
Mutate_delete
Mutate_insert
Mutate_replace
N
Neighbour_at(om)
Neighbour_re(sidue)
NCS overview
NCS_add_maps
NCS_average
NCS_map_writ(e)
NCS_mask_ed(it)
NCS_mask_lay(er)
NCS_mask_mak(e)
NCS_mask_sph(ere)
NCS_mask_wri(te)
NCS_operator
NCS_instance
NCS_sphere
No
Note Overview
Note_id_add
Note_name
Note_object
Note_setup
Note_sphere
Note_xyz_add
O
O descriptor language
O_setup
Object_name
P
Paint Overview
Paint_case
Paint_colour
Paint_map
Paint_obj_at(om)
Paint_obj_zo(ne)
Paint_object
Paint_property
Paint_ramp
Paint_select
Paint_zone
Patterson Overview
Patt_cross
Patt_move
Patt_setup
PDB_kill
PDB Overview
PDB_read
PDB_write
Pep_Flip
Phi_Psi
Plotting Overview
Plot
Plot_off
Plot_on
Plot_setup
Pop-up
Print
Q
QDS overview
QDS_atom
QDS_extend
QDS_extract
QDS_ring
QDS_setup
QDS_undo
QDS_write
Quit
R
Read_formatt(ed)
Refi Overview
Refi_alterna(te)
Refi_clear_a(tom)
Refi_clear_g(roup)
Refi_continu(ous)
Refi_fix_atom
Refi_geometry
Refi_generat(e)
Refi_init
Refi_patch
Refi_zone
Render
Ring_Plane
Ring_Distanc(e)
Ring_to_ring
Rot_Trans_Ob(j)
Rot_Trans_DB
Rotate_picture
RS_fit
RSC_fit
S
Sam_init_db
Sam_list_seq
Sam_rename
Save_DB
Screen_colour
Select Overview
Select_invert
Select_object
Select_off
Select_on
Select_property
Select_visible
Skeleton
Sketch Overview
Sketch_add
Sketch_auto
Sketch_cpk
Sketch_lighting
Sketch_object
Sketch_setup
Sketch_stick
Sketch_type
Sketch_undo
Slider_show
Spawn
Sphere_centre
Spin
Sprout overview
Sprout_auto
Sprout_CAT
Sprout_easy
Sprout_grow
Sprout_setup
Sprout_sst
Sprout_trace
SST Overview
SST_build
SST_combine
SST_extend
SST_flip
SST_merge
SST_reverse
SST_trim
SST_zap
Stereo
Stop
Symbol
Symbol_define
Symbol_delet(e)
Symbol_incre(ment)
Symbol_list
Symmetry Overview
Symm_cell
Symm_instance
Symm_setup
Symm_sphere
T
Terminal_ID
Tor_general
Tor_residue
Trig_refresh
Trig_reset
U
Undo_read
Undo_write
V
Visible_object
W
Wait_ID
Water Overview
Water_add
Water_electr(ons)
Water_peak
Water_prof(ile)
Water_sort
Water_tidy
Window_open
Write_formatted
Y
YASSPA
Yes
Z
Zone

Pull-downs
Pull-down Overview
Controls
Display
Display/Paint
Display/Sketch
Graph
Graph/Molecule
Graph/Graph Y DB
Graph/Graph X DB
Graph/Graph It
Graph/Ramachandran
Graph/Sequence
Rebuild
Rebuild/Grab
Rebuild/Torsion
Rebuild/Regularize
Rebuild/Database
Rebuild/Trig
Rebuild/Mutate
Rebuild/Insert
Bones
Bones/Set to class
Bones/Baton
Density
Density/Slider
Density/Density
Density/2ry unit
Density/Template
Density/E.D. Fit
Menus

Master menu
Master
Rebuild
QDS
Fonts
Skeletons

Gone
No longer available
Water_add
(replaced by a totally new command of the same name)
Water_init
Water_pekpik

Best forgotten
Baton_build
Baton_mode
Map Overview
Map_Active_C(entre)
Map_Atom_Cen(tre)
Map_Cache
Map_Cover
Map_Draw
Map_File
Map_Informat(ion)
Map_Object
Map_Paramete(rs)
Map_Xyz_Cent(re)
Mask Overview
Mask_contour
Mask_object
Mask_off
Mask_on
Mask_read
Mask_setup
Mask_write
Move Overview
Move_atom
Move_fragment
Qmap_draw
Qmap_file
Qmap_setup
Qmap_zap

RSR overview
RSR_contours
RSR_dgnl
RSR_map
RSR_rigid
RSR_rotamer
RSR_scale
RSR_setup
RSR_zone
Sam Overview
Sam_atom_in
Sam_atom_out
Slider Overview
Slider_combine
Slider_display
Slider_guess
Slider_lego
Slider_setup
Trace_fill_Ca
Trace_prune
Trace_setup
Trace_sphere
Macros in DB
@on_baton_yes
@on_escape
@on_graph_pick
@on_rama_pick
@on_trace_draw
@pt_blue_red
@pt_by_atom
@pt_by_b
@pt_red_blue
@sph_id