Index

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Index

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.active_centre: Sphere_centre, Datablocks, Map_Active_Centre, Water_add, Centre_atom, Centre_XYZ, Rot_trans_Db, Symm_sphere, Examples
.active_colour: Paint_colour
.active_colour_name: Paint_colour
.active_surface: A note on , A note on
.bones_colour: The Bones commands
.cell_odl: Symm_cell
.colour_names: Personalized Colours
.colour_rgb: Personalized Colours
.cpk_radii.o: Sketch_cpk
.default_formats: Write_formatted
.draw_symobj: Symm_object
.id_a: Symbols
.id_m: Symbols
.id_r: Symbols
.id_template: Customizing the message , Customizing the message
.id_z: Symbols
.lsq_integer: Datablocks for the
.lsq_rt_: Lsq_object, Lsq_molecule
.manip_integer: Datablocks used by
.map_c6: Datablocks for the
.map_integer: Datablocks for the
.map_real: Datablocks for the
.mask_c6: Datablocks
.menu: Menus, Menu_control
.menu_integer: Menu_control
.menu_real: Menu_control
.message_template: Customizing the message , Customizing the message
.molec_obj_integer: Datablocks, The Trig commands
.moving_atom: Move_atom
.obj_3dt_ca: Datablocks
.obj_col_ca: Datablocks
.obj_con_ca: Datablocks
.obj_idx_ca: Datablocks
.refi_c6: Datablocks for the
.refi_dict: Datablocks for the
.refi_real: Datablocks for the
.rsr_dict_XXX: Datablocks used by
.slider_integer: Datablocks Used
.slider_matrix: Datablocks Used
.slider_real: Datablocks Used
.solid_hbonds: Datablock used
.stick_radius: Sketch_stick
.torsion_information: Tor_residue, Tor_residue, Datablocks used by
.trig_real: Neighbour_atom, Neighbour_residue, Datablock used
O database: The O_heap_1 commands
O files, input: Read_formatted
O files, output: Write_formatted
O database: The O_heap_2 commands
dispcol: Personalized Colours
mkcol: Personalized Colours
_atom_b: Mutate_replace
_atom_bone: Customizing the message
_atom_colour: Mutate_replace
_atom_name: Paint_case, Mutate_replace
_atom_select: The Select commands, Patterson
_atom_wt: Mutate_replace
_atom_xyz: The O database
_atom_z: Mutate_replace
_residue_2ry_struc: YASSPA
_residue_irc: Paint_ramp
_residue_pepflip: Examples, Pep_flip
_residue_rsc: RSC_fit
_residue_rsfit: RS_fit
_residue_type: The O database
A programs: The averaging programs
Active_Centre: Map_Active_Centre
all.dat: Getting started... , Connect_file, Examples
alpha.o: YASSPA
amino acid, size: Slider_lego
Angle_define: Angle_define
Arith_Db: Arith_Db
arrow: The Sketch commands
arrow key: SGI 4D extensions
average: The averaging programs
averaging: The averaging programs
Backup_DB: The Manip menu, Backup_DB
Baton_build: Baton_build
Baton_mode: Baton_mode
Bell: Bell
beta.o: YASSPA
Bone_branch: Bone_branch
Bone_break_bond: Bone_break_bond
Bone_Ca_Id: Bone_Ca_Id, Baton_build
Bone_Ca_zone: Bone_Ca_zone
Bone_draw: Bone_draw
Bone_excise: Bone_excise
Bone_make_bond: Bone_make_bond
Bone_mask: Bone_mask
Bone_prune: Bone_prune
Bone_redefine: The Bones commands, Bone_redefine, Bone_mask
Bone_repeat: Bone_repeat
Bone_setup: Bone_setup
Bone_skip: Bone_skip
Bone_undo: Bone_undo
bones: The Bones commands, The Bones commands
bones_mask: The averaging programs
brix: Map_File, Map_info, Brix --- yet
Ca_zone: Ca_zone
CCP4: Map_File, The Sam commands
CCP4 map: The Quick Map
Centre_atom: Sphere_centre, Centre_atom
Centre_ID: Sphere_centre, Centre_ID
Centre_next: Centre_next
Centre_prev: Centre_prev
Centre_XYZ: Sphere_centre, Centre_XYZ
Centre_zone: Sphere_centre, Centre_zone
Clear_flag: Move_atom, Move_zone, Move_fragment, Move_object, Trig_refresh
Clear_flags: Phi_Psi, Clear_flags
Clear_Id: Clear_Id
colcod macro: The Paint commands
colour code: The Paint commands
colour, of objects: The Paint commands
colours, available: dispcol
colours, personalized: Personalized Colours
Connect_file: Connect_file
connectivity file: Connect_file
coordinate files: The Sam commands
coordinate input: Sam_atom_in
coordinate output: Sam_atom_out
coordinate system: Map_Xyz_Centre
Copy_Db: Copy_Db
Cover_sphere: Cover_sphere
CPK models: Sketch_cpk
CPK_object: Sketch_cpk, Cpk_object
crystallographic symmetry: The Symmetry commands
cutoff, in lsq: Macros
cylinder: The Sketch commands
Db_create: Db_create
Db_delete: Db_delete
Db_kill: Db_kill
DB_stat: DB_stat
Db_table_residue: Db_table_residue
Delete_object: Delete_object, The Map commands
density modification: The averaging programs
dial set: The Manip menu
Dial_box: Dial_box
Dial_next: Dials, The Manip menu, Tor_residue, Dial_next
Dial_previous: Dials, The Manip menu, Tor_residue, Dial_previous
dialbox: Dials
dialbox.o: Dial_next
Diamond files: The Sam commands
Directory: Directory
dispcol: dispcol
Dist_define: Dist_define, Example
Draw_object: Objects, Draw_object
electron density map: The Map commands
End_object: The Draw_Mol commands, End_object
envelope: Mask Commands
EZD: The Quick Map
EZD map format: EZD_map
EZD_draw: EZD_draw
EZD_map: EZD_map
file_o_backup: Backup_DB
file_o_save: Save_DB, Datablocks
file_refi_dict: Datablocks for the
Flip_peptide: Flip_peptide
fragment dictionary: RSR_zone
hardcopy: The Plot commands
Hbonds_all: Hbonds_all
Hbonds_mc: Hbonds_mc
Help: Help
hydrogen bonds: Hbonds_mc, Hbonds_all
ID label, customizing: Customizing the message
Lego_Auto_MC: Lego_Auto_MC
Lego_Auto_SC: Lego_Auto_SC
Lego_bones: Lego_bones
Lego_Ca: Lego_Ca, RSR_dgnl
Lego_loop: The Select commands, Lego_Loop, Mutate_insert
Lego_setup: Lego_setup, Mutate, Mutate_replace, RSC_fit
Lego_side: Mutate_insert
Lego_Side_Chain: Lego_Side_Chain
Lsq_explicit: Lsq_explicit
Lsq_improve: Lsq_improve, Lsq_paired_atoms, Macros
Lsq_mol: Datablocks for the
Lsq_molecule: Lsq_molecule
Lsq_obj: Datablocks for the
Lsq_object: Lsq_object
Lsq_paired_atoms: Lsq_paired_atoms
macro bones_50a: Macros
macro change_save_file: Save_DB
macro save_as: Save_DB
macro symmetry_molecules: Symm_object, Datablocks
main chain database: The Lego commands
main chain, building: Lego_Auto_MC
Manip: The Manip menu
Map_Atom_Centre: Map_Atom_Centre
Map_Cache: The Map commands, Map_Cache
Map_cover: Map_cover
Map_draw: Map_draw, Map_cover
Map_File: Map_File
Map_info: Map_info
Map_object: Map_object
Map_param: Map_param
mappage: Map_File, Brix --- yet
mask editing: Mask Commands
mask, from skeleton: The averaging programs
Mask_contour: Mask_contour
Mask_object: Mask_object
Mask_off: Mask_off
Mask_on: Mask_on
Mask_read: Mask_read
Mask_setup: Mask_setup
Mask_write: Mask_write
menu.o: Menus
Menu_control: Menus, Menus, Menu_control
menu_mutate.o: Example: menu_mutate.o
menus: Menus
Merge_atoms: Merge_atoms
Message: Message
message text, customizing: Customizing the message
mkcol: mkcol
Molecular Replacement: MolRep -- Molecular
Molecule_name: The Draw_Mol commands, Molecule_name
MolRep: MolRep -- Molecular
mouse buttons: SGI 4D extensions
Move_atom: The Manip menu, Move_atom, Example
Move_fragment: The Select commands, Move_fragment, The RSR dictionary
Move_object: Move_object
Move_zone: Dials, The Manip menu, Move_zone
moving atom: Patt_move
MR_rt: MR_rt
MR_setup: MR_setup
Mutate: Mutate
Mutate_delete: Mutate_delete
Mutate_insert: Mutate_insert
Mutate_replace: Mutate_replace
Mutate_setup: Mutate_setup
Neighbour_atom: Neighbour_atom
Neighbour_residue: Neighbour_residue
No: No
Note_id_add: Note_id_add
Note_name: Note_name
Note_object: Note_object
Note_setup: Note_setup
Note_sphere: Note_sphere
Note_xyz_add: Note_xyz_add
nucleic acids: Symbols
o.dat: Connect_file, Examples
O_moving_atom: Examples
O_setup: O_setup
Object_name: The Draw_Mol commands, Object_name
objects: The special major
On_off: Objects, On_off
oplot: Sketch_setup, The Plot commands, oplot
oplot input: The oplot input
oplot output: The oplot output
overlaying structures: The LSQ commands
Paint_case: Paint_case
Paint_colour: The Paint commands, The Paint commands, Paint_colour
Paint_obj_atom: Paint_obj_atom
Paint_obj_zone: The Paint commands, Paint_obj_zone
Paint_object: The Paint commands, Paint_object
Paint_property: The Paint commands, Paint_property
Paint_ramp: Paint_ramp
Paint_select: Paint_select, The Select commands
Paint_zone: The Paint commands, Paint_zone
parser: The command line , The command line , Symbols
Patt_cross: The Select commands, Patt_cross
Patt_move: Move_atom, Patt_move
Patt_setup: Patt_setup
Patterson: Patterson
PDB files: The Sam commands
Pep_flip: Examples, Pep_flip
PHASES: The Quick Map , The Sam commands
Phi_Psi: Phi_Psi
Plot: Plot
Plot commands: The Plot commands
Plot_off: Plot_off
Plot_on: Plot_on
Plot_setup: Plot_setup
plotting: oplot
plotting, in stereo: Plot_setup
Print: Print
PROLSQ: The Sam commands
PROTEIN: Map_File, The Sam commands
protein building blocks: The Lego commands
Qm_draw: Qm_draw
Qm_file: Qm_file
Qm_setup: Qm_setup
Qm_zap: Qm_zap
Quit: Quit
radii.o: Sketch_cpk
rattler: The Sketch commands
RAVE: Bone_mask, The averaging programs
Read_formatted: Menus, Examples, Menu_control, Read_formatted
real space correlation: RS_fit
real space fit: RS_fit
real space refinement: The RSR commands
Refi_setup: Refi_setup
Refi_zone: Refi_zone
regularisation: The Refi commands
residue_dict.o: Hbonds_all
RGB colour: Paint_colour
ribbon: The Sketch commands
Rot_Tran_Obj: Datablocks for the , Rot_Tran_Obj
Rot_trans_Db: Rot_trans_Db
rotamer database: The Lego commands
Rotate_picture: Rotate_picture
RS_fit: RS_fit
RSC_fit: RSC_fit
rsfit_all.o: RS_fit
rsfit_mc.o: RS_fit
RSR: The RSR commands
RSR, dictionary: The RSR dictionary
RSR_contours: RSR_contours
RSR_dgnl: RSR_dgnl
rsr_dict.o: RSR_zone
RSR_dict_: RSR_zone, The RSR dictionary
RSR_map: RSR_map, RS_fit
RSR_rigid: RSR_rigid
RSR_rotamer: RSR_rotamer
RSR_scale: RSR_scale
RSR_setup: RSR_setup
RSR_zone: RSR_zone
Sam_atom_in: Sam_atom_in
Sam_atom_out: The Select commands, Sam_atom_out
Sam_init_db: Connect_file, Sam_init_db
Sam_list_sequ: Sam_list_sequ
Sam_rename: Sam_rename
Save_DB: Bone_break_bond, Bone_make_bond, Stop, Save_DB
Screen_colour: Screen_colour
Select_invert: Select_invert
Select_off: Select_off
Select_on: Select_on, Lego_Loop
Select_property: Select_property, Examples
Select_visible: The Select commands, Select_visible
sequence, fitting: Slider
set_atom: Db_set_atom
set_data: Db_set_data
set_zone: Db_set_zone
side chains, building: Lego_Auto_SC
single atom: The O database
skeleton: The Bones commands
skeleton filters: Trace Commands
Sketch_add: Sketch_add, Sketch_undo
Sketch_auto: Sketch_auto
Sketch_cpk: Sketch_stick, Sketch_cpk
Sketch_object: Sketch_object
Sketch_setup: Sketch_setup, Sketch_setup, Sketch_auto, Sketch_auto
Sketch_stick: Sketch_stick, Sketch_cpk
Sketch_type: The Sketch commands, Sketch_setup, Sketch_type
Sketch_undo: Sketch_undo
Slider: Slider
Slider matrix: Slider_guess
Slider_combine: Slider_combine
Slider_display: Slider_display
Slider_guess: Slider_guess
Slider_lego: Slider_lego, Baton_build
Slider_setup: Slider_setup
Slider_show: Slider_show
spacegroup, defining: Symm_setup
Spawn: Spawn
Sphere_centre: Sphere_centre, Datablocks
Spin: Spin
spiral: The Sketch commands
startup.o: Dial_next
Stereo: Stereo
stick representation: Sketch_stick
Stop: Stop
Symbols: Symbols
Symbols, predefined: Symbols
Symm_cell: Symm_cell
Symm_object: Symm_object
Symm_setup: Symm_setup
Symm_sphere: Symm_sphere
tapeworm: The Sketch commands
Term_id: Dist_define, Angle_define
Terminal_ID: Terminal_ID
TNT: The Quick Map
Tor_general: Tor_general
Tor_residue: Tor_residue
torsion.o: Tor_residue
Trace commands: Trace Commands
Trace_fill_Ca: Trace_fill_Ca
Trace_prune: Trace_prune
Trace_setup: Trace_setup
Trig_refresh: Trig_refresh, Example
Trig_reset: Trig_reset
unit cell, defining: Symm_setup
unit cell, drawing: Symm_cell
update;tex2html_html_special_mark_quot;macro: Menus
visibility: Examples
Wait_ID: Wait_ID
water molecules: Water_pekpik
Water_add: Water_add
Water_init: Water_init
Water_pekpik: Water_pekpik
Write_formatted: Menus, Menu_control, Write_formatted
X-PLOR: Map_File, The Quick Map , The Sam commands
Xyz_Centre: Map_Xyz_Centre
Yes: Yes
yes_no: If_yes_no
Zone: Zone, Examples