Internal GUI (the panels PyMOL draws inside the viewport)

Scope: everything PyMOL draws itself inside the OpenGL viewport as 2D “Blocks” — the right-hand object panel (“names list”), its A/S/H/L/C/M popup menus, the mouse-mode block, the movie/frame control bar, the movie timeline panel, the in-scene scene bar, the wizard panel, the in-viewport command prompt + feedback scrollback, the popup-menu engine itself, the busy/progress box and the splash. Read-only source analysis of packages/engine/, which is unmodified upstream. All line references were opened and read. Where the port stands. The internal GUI is turned off in the engine (internal_gui 0, internal_feedback 0 at bridge boot) and rebuilt as components: object panel apps/web/src/features/objects/, popup menus apps/web/src/features/pymol-menu/, mouse-mode block apps/web/src/features/mouse/ButModeBlock.tsx, transport + timeline apps/web/src/features/movie/, scene bar apps/web/src/features/scenes/, wizard block apps/web/src/features/wizards/, prompt + scrollback + busy overlay apps/web/src/features/console/. The layout of §0 is reproduced in apps/web/src/shell/orthoPanel.ts and apps/web/src/shell/extGuiDock.ts.

0. Layout model

OrthoLayoutPanel() — packages/engine/layer1/Ortho.cpp:2261-2340 — stacks the internal-GUI blocks in a right-hand column, bottom-up:

Block	Height	Source
Control (movie buttons)	`DIP2PIXEL(20)`	`packages/engine/layer1/Ortho.cpp:2267`, `packages/engine/layer1/Ortho.cpp:2296-2299`
ButMode (mouse mode)	`ButModeGetHeight()` = `DIP2PIXEL(124)` if `mouse_grid` else `DIP2PIXEL(40)`	`packages/engine/layer1/ButMode.cpp:72-77`
Wizard	`internal_gui_control_size * NLine + 4`, 0 if no wizard	`packages/engine/layer1/Wizard.cpp:254-259`
Executive (object panel)	everything above, to the top of the window	`packages/engine/layer1/Ortho.cpp:2280-2284`

Column width = internal_gui_width (default cOrthoRightSceneMargin = DIP2PIXEL(220), packages/engine/layer1/SettingInfo.h:182, packages/engine/layer1/Ortho.h:24). The whole column is suppressed when internal_gui = 0 (packages/engine/layer1/Ortho.cpp:2286-2312, packages/engine/layer1/SettingInfo.h:183). OrthoReshape() — packages/engine/layer1/Ortho.cpp:2340-2463 — additionally computes:

textBottom = MovieGetPanelHeight(G) (movie timeline height) — packages/engine/layer1/Ortho.cpp:2385-2386
sceneBottom = textBottom + (internal_feedback-1)*cOrthoLineHeight + cOrthoBottomSceneMargin when internal_feedback is set — packages/engine/layer1/Ortho.cpp:2388-2393
sequence viewer above or below the scene depending on seq_view_location / seq_view_overlay — packages/engine/layer1/Ortho.cpp:2413-2442
cOrthoLineHeight = DIP2PIXEL(12), cOrthoCharWidth = DIP2PIXEL(8), cOrthoLeftMargin = DIP2PIXEL(3), cOrthoBottomMargin = DIP2PIXEL(5) — packages/engine/layer1/Ortho.h:26, packages/engine/layer1/Ortho.cpp:62-64

internal_gui_mode (packages/engine/layer1/SettingInfo.h:436, enum packages/engine/layer0/PyMOLEnums.h:33-38): Default (0, opaque panel reserves screen space), BG (1), Transparent (2, panel floats over the scene and does not reserve space — packages/engine/layer1/Ortho.cpp:2400-2405). Mouse-event routing: OrthoButton() — packages/engine/layer1/Ortho.cpp:2493-2563 — finds the topmost Block at (x,y) (COrtho::findBlock, packages/engine/layer1/Ortho.cpp:2980-2991), honours a “grab” (OrthoGrab/OrthoUngrab, packages/engine/layer1/Ortho.cpp:1191-1221), and dispatches click/drag/release. OrthoDrag() — packages/engine/layer1/Ortho.cpp:2575-2607. Modifier bit masks: cOrthoSHIFT 1, cOrthoCTRL 2, cOrthoALT 4 — packages/engine/layer1/Ortho.h:20-22.

1. Object panel (“names list”, the Executive block)

Implementation: CExecutive::draw packages/engine/layer3/Executive.cpp:16167-16559, CExecutive::click packages/engine/layer3/Executive.cpp:14994-15424, CExecutive::drag packages/engine/layer3/Executive.cpp:15661-16013, CExecutive::release packages/engine/layer3/Executive.cpp:15560-15658, CExecutive::reshape packages/engine/layer3/Executive.cpp:16593-16602.

1.1 Row model

Rows come from CExecutive::Panel, a std::vector<PanelRec> (packages/engine/layer3/ExecutiveDef.h:20-31, packages/engine/layer3/ExecutiveDef.h:79) rebuilt by ExecutiveUpdatePanelList() packages/engine/layer3/Executive.cpp:1565-1577. Each PanelRec carries spec (the SpecRec), nest_level, is_group, is_open. SpecRec (packages/engine/layer3/SpecRec.h:9-37) fields that drive the row:

type — cExecAll (the synthetic “all” row), cExecObject, cExecSelection
name, obj, visible (“enabled”, not “visible”), group_name, group
hilight — 0 none, 1 name button pressed, 2 group +/- pressed
sele_color, in_scene, in_panel, grid_slot

Row height = internal_gui_control_size px (default 18, packages/engine/layer1/SettingInfo.h:411); ExecLineHeight is read per draw at packages/engine/layer3/Executive.cpp:16192-16193.

1.2 What a row draws (left→right)

Scroll bar on the far left when n_ent > n_disp (packages/engine/layer3/Executive.cpp:16222-16255, 16266-16272); width ExecScrollBarWidth = DIP2PIXEL(13), margin DIP2PIXEL(1) — packages/engine/layer3/Executive.cpp:6090-6091.
Group open/close button [+] / [-], DIP2PIXEL(15) wide, only when panel->is_group — packages/engine/layer3/Executive.cpp:16411-16437. - when open, + when closed.
Indent nest_level * DIP2PIXEL(8) — packages/engine/layer3/Executive.cpp:16399.
Name button (a 3D-bevel rect, draw_button() packages/engine/layer3/Executive.cpp:16015-16098). Fill colour:
- pressed / hovered: pressedColor {0.7,0.7,0.7}
- enabled (and all ancestor groups enabled): enabledColor {0.5,0.5,0.5}
- enabled but an ancestor group is disabled: cloakedColor {0.35,0.35,0.35}
- disabled: disabledColor {0.25,0.25,0.25} — packages/engine/layer3/Executive.cpp:16173-16176, 16439-16461.
Name text. Selections are wrapped in ( ). If the name is prefixed by its group name and group_full_member_names=0 (packages/engine/layer3/Executive.cpp:16196), the prefix is stripped; with group_arrow_prefix=1 (:16197) a ^| glyph is drawn instead. Text colour from getNameColor() packages/engine/layer3/Executive.cpp:16117-16164 driven by internal_gui_name_color_mode (0 default text colour, 1 first carbon atom colour, 2 object colour; falls back to default if within 0.1 of the button colour).
Caption in captionColor {0.3,0.9,0.3} (packages/engine/layer3/Executive.cpp:16179) after the name, for objects only — drawn at :16532-16545. Content from CObject::getCaption(); only ObjectMolecule implements it (packages/engine/layer2/ObjectMolecule.cpp:386-460, base returns nullptr packages/engine/layer1/PyMOLObject.h:135) producing "<coordset name> <colorcode><state>/<nstates>", colour-coded \789 when the object has a frozen state setting and \993 when discrete, controlled by state_counter_mode.
A S H L C (M) toggle buttons on the right, each ExecToggleWidth = DIP2PIXEL(17) wide, ExecToggleSize = DIP2PIXEL(16) — packages/engine/layer3/Executive.cpp:3280-3281, drawn at packages/engine/layer3/Executive.cpp:16312-16390. Button count is get_op_cnt(): 5 normally, 6 (adds “M”) when button_mode_name == "3-Button Motions" — packages/engine/layer3/Executive.cpp:1757-1764. Per-button fills: A {0.5,0.5,1.0}, S {0.6,0.6,0.8}, H {0.4,0.4,0.6}, L {0.5,0.5,1.0}, C = rainbow gradient (nullptr inside → 4-colour quad, packages/engine/layer3/Executive.cpp:16074-16090), M = colour by motion “spec level” (0→{0.4,0.4,0.6}, 1→{0.6,0.6,0.8}, 2→activeColor {0.9,0.9,1.0}, :16182) — packages/engine/layer3/Executive.cpp:16369-16390. These buttons are compiled out entirely under _PYMOL_NOPY (packages/engine/layer3/Executive.cpp:16306) because they call Python for their menus.

Panel background/edge and the 1px separator line at Width - internal_gui_width: OrthoDrawInternalGUIBG() packages/engine/layer1/Ortho.cpp:1561-1584.

1.3 Click semantics on the toggle buttons

CExecutive::click packages/engine/layer3/Executive.cpp:14994-15424. The hit column index t = (rect.right - x - 1) / ExecToggleWidth, then t = op_cnt - t - 1, giving 0=A, 1=S, 2=H, 3=L, 4=C, 5=M. Each dispatches MenuActivate* with a Python menu-builder name from packages/engine/modules/pymol/menu.py and the row’s object/selection name (namesele):

Btn	Row type / object type	Menu function called
A	`cExecAll`	`all_action` (`Executive.cpp:15070`)
A	selection	`sele_action` (`:15073`)
A	group	`group_action` (`:15079`)
A	molecule	`mol_action` (`:15083`)
A	map	`map_action` (`:15087`)
A	surface	`surface_action` (`:15091`)
A	mesh	`mesh_action` (`:15095`)
A	measurement / CGO / callback / alignment / volume	`simple_action` (`:15103`)
A	slice	`slice_action` (`:15107`)
A	gadget (ramp)	`ramp_action` (`:15111`)
S	all	`mol_show` with `"all"` (`:15120`)
S	selection, group, molecule	`mol_show` (`:15123`, `:15129`)
S	CGO / alignment	`cgo_show` (`:15133`)
S	measurement	`measurement_show` (`:15137`)
S	map	`map_show` (`:15140`)
S	mesh	`mesh_show` (`:15143`)
S	surface	`surface_show` (`:15147`)
S	slice	`slice_show` (`:15151`)
S	volume	`volume_show` (`:15155`)
H	(mirror of S)	`mol_hide`/`cgo_hide`/`measurement_hide`/`map_hide`/`mesh_hide`/`surface_hide`/`slice_hide`/`volume_hide` (`:15164-15198`)
L	all	`mol_labels` with `"(all)"` (`:15208`)
L	selection, group, molecule	`mol_labels` (`:15211`, `:15218`)
L	measurement / map / surface / mesh / slice	no menu (empty cases, `:15220-15227`)
C	all, selection, group, molecule	`mol_color` (`:15235`, `:15241`)
C	map / CGO / alignment	`general_color` (`:15247`)
C	mesh	`mesh_color` (`:15251`)
C	surface	`mesh_color` with 2nd arg `"surface"` (`:15254`)
C	measurement	`measurement_color` (`:15259`)
C	slice	`slice_color` (`:15263`)
C	volume	`vol_color` (`:15266`)
C	gadget	`ramp_color` (`:15270`)
M	all	`camera_motion` (0 args) (`:15279`)
M	selection	nothing (`:15281`)
M	group/molecule/measurement/map/surface/CGO/mesh	`obj_motion` (`:15294`)

MenuActivate* (packages/engine/layer4/Menu.cpp:29-124) calls pymol.menu.<name>(cmd, *args) and feeds the returned list to PopUpNew.

1.4 Click semantics on the name / group control

packages/engine/layer3/Executive.cpp:15300-15412:

Hit test: “on the name” when (xx-1)/DIP2PIXEL(8) > nest_level (> nest_level+1 for groups); otherwise “on the group control”.
Left button on name → DragMode=Visibility, ToggleMode=DeferVisibility (toggle is applied on release). Modifier variants:
- Shift+Ctrl → HoverActivate + zoom-on-hover; immediately enables the row and ExecutiveWindowZoom (:15323-15334)
- Shift → ImmediateVisibility, toggles at once (:15336-15337)
- Ctrl → HoverActivate (enable-only, exclusive-ish) (:15338-15344)
Middle button on name → DragMode=VisibilityWithCamera:
- plain → CenterActivateDeactivatePrevious, runs ExecutiveCenter (:15376)
- Ctrl → ZoomActivateDeactivatePrevious, runs ExecutiveWindowZoom (:15362)
- Ctrl+Shift → ZoomExclusiveActivate: ExecutiveSetObjVisib("all", false) then enable only this row (:15368)
Right button on name → DragMode=Reorder (drag to reorder / re-group) (:15392).
Left on group [+]/[-] → hilight=2, PressedWhat=2; on release logs cmd.group("<name>",action='open'|'close') and calls ExecutiveGroup(...,5,1) — packages/engine/layer3/Executive.cpp:15620-15627.
Mouse wheel anywhere in the panel scrolls the list by ±1 row — packages/engine/layer3/Executive.cpp:15017-15023.
When internal_gui_mode != Default and y < HowFarDown (below the last row), the click is forwarded to the Scene block — packages/engine/layer3/Executive.cpp:15010-15014.

Drag-visibility band-select: dragging vertically toggles every row between Pressed and Over (packages/engine/layer3/Executive.cpp:15727-15809). Reorder drag emits cmd.order("<a> <b>", location="upper"|"current") and/or group <parent>, <child> / ungroup <child> — packages/engine/layer3/Executive.cpp:15928-15960. Release path: ExecutiveSpecSetVisibility() packages/engine/layer3/Executive.cpp:15474-15541 is the single mutation point; it logs cmd.enable('x') / cmd.disable('x') / cmd.enable('all') / cmd.disable('all'), respects active_selections (hides other selections when one is enabled) and calls SceneObjectAdd/Del.

1.5 Panel-level behaviours

hide_underscore_names (default 1, packages/engine/layer1/SettingInfo.h:558) hides _-prefixed recs.
ExecutiveManageObject sets visible=1 for new objects except maps (visible=0) — packages/engine/layer3/Executive.cpp:14885-14894.
auto_hide_selections / auto_show_selections (defaults 1/1, packages/engine/layer1/SettingInfo.h:162-163) — packages/engine/layer3/Executive.cpp:14841, 14982-14986.
group_auto_mode auto-creates/attaches groups from dotted names — ExecutiveDoAutoGroup packages/engine/layer3/Executive.cpp:14766-14811.

Menu data model: a Python list of [code, text, command] (packages/engine/layer4/PopUp.cpp:226-249), where code is 0 = separator bar, 1 = clickable item, 2 = non-clickable title/label (packages/engine/layer4/PopUp.cpp:270-300, drawn packages/engine/layer4/PopUp.cpp:865-880). command is either a Python source string (executed by PParse on release, packages/engine/layer4/PopUp.cpp:471-475) or a nested list / a zero-arg callable that lazily returns a list (SubGetItem, packages/engine/layer4/PopUp.cpp:88-110). Text may embed 4-char colour codes \RGB with digits 0-9 (TextStartsWithColorCode packages/engine/layer1/Text.cpp:507-521, TextSetColorFromCode packages/engine/layer1/Text.cpp:530-548; \--- resets to the default colour). All contents below live in packages/engine/modules/pymol/menu.py.

2.1 Action menus

all_action (menu.py:1497-1518): zoom / center / origin — separator — preset ▸ / find ▸ — separator — hydrogens ▸ / remove waters — separator — delete selections (map(cmd.delete,cmd.get_names("selections"))) — separator — delete everything (cmd.delete("all")) — separator — masking ▸ / movement ▸ / compute ▸. sele_action (menu.py:1160-1188): delete selection, rename selection (cmd.wizard("renaming",...)) — zoom / orient / center / origin — drag coordinates (cmd.drag) / clean — modify ▸ / preset ▸ / find ▸ / align ▸ — remove atoms (cmd.remove(...) + cmd.delete(...)) / hydrogens ▸ — duplicate (cmd.select(None,...)) / copy to object ▸ (lazy) / extract object (cmd.extract(None,...)) — masking ▸ / movement ▸ / compute ▸. sele_action2 (menu.py:1191-1214) — the variant used from in-scene picking menus: same head, then preset/find, remove atoms, then around/expand/extend/invert/complete inline, then duplicate selection/copy to object/extract object, masking/movement/compute. mol_action (menu.py:1248-1281): zoom/orient/center/origin — drag matrix (cmd.drag) / reset matrix (cmd.reset(object=…)) — drag coordinates / clean — preset ▸ / find ▸ / align ▸ / generate ▸ — assign sec. struc. (cmd.dss) — rename object / copy to object ▸ / group ▸ / delete object — hydrogens ▸ / remove waters — state ▸ / masking ▸ / sequence ▸ / movement ▸ / compute ▸. group_action (menu.py:1217-1246): zoom/orient/center/origin — drag / reset — preset ▸ / find ▸ / align ▸ / generate ▸ — assign sec. struc. — rename group / group ▸ / delete group — hydrogens ▸ / remove waters — state ▸ / masking ▸ / sequence ▸ / movement ▸ / compute ▸. map_action (menu.py:1384-1405): mesh ▸ / surface ▸ / slice ▸ / gradient ▸ / volume ▸ — zoom / center / origin — drag / reset — matrix_copy ▸ — rename / group ▸ — delete. mesh_action (menu.py:1443-1458) and surface_action (menu.py:1426-1441): level ▸ — zoom / center / origin — drag / reset — rename / group ▸ — delete. slice_action (menu.py:1283-1302): zoom / center / origin — tracking on|off (slice_track_camera) — height map on|off (slice_height_map) — dynamic grid on|off (slice_dynamic_grid) — rename / group ▸ — delete. simple_action (menu.py:1304-1318): zoom / center / origin — drag / reset — rename / group ▸ — delete. ramp_action (menu.py:1460-1471): levels ▸ with Range +/- L for L ∈ {0.1,0.2,0.5,1,2,5,10,20,50,100} → cmd.ramp_update(name, range=[-L,L]) — group ▸ — delete. Shared action sub-menus:

presets (menu.py:728-747): classified, simple, simple (no solvent), ball and stick, b factor putty, technical, ligands, ligand sites ▸, pretty, pretty (with solvent), publication, publication (with solvent), protein interface, default — all preset.*("<sele>"). preset_ligand_sites (menu.py:714-726): cartoon, solid surface, solid (better), transparent surface, transparent (better), dot surface, mesh surface.
hydrogens (menu.py:749-755): add / add polar / remove / remove nonpolar.
state (menu.py:757-766): freeze / all states / thaw / split (cmd.split_states).
movement (menu.py:768-772): protect / deprotect.
sequence (menu.py:774-780): include / exclude / default (seq_view object setting).
masking (menu.py:782-786): mask / unmask.
compute (menu.py:788-807): atom count; charges ▸ (formal charge sum, partial charges sum); surface area ▸ (molecular, solvent accessible, per residue rel. sol. acc.); molecular weight ▸ (explicit, with missing hydrogens).
mol_generate (menu.py:854-860): selection ▸ (selection, menu.py:840-852: all, polymer, organic, solvent, polar hydrogens, non-polar hydrogens, donors, acceptors, surface atoms, C-alphas), symmetry mates ▸ (symmetry, menu.py:821-833: cmd.symexp within 4/5/6/8/12/20/50/100/250/1000 Å), vacuum electrostatics ▸ (vacuum, menu.py:809-819: protein contact potential (local) + 4 note lines).
find (menu.py:1050-1064): polar contacts ▸ (polar, menu.py:1004-1047, 12 entries from “within selection” to “between chains”), any contacts ▸ (3.0/3.5/4.0 Å), halogen-bond interactions ▸, salt-bridge interactions ▸, pi interactions ▸ (all / pi-pi / pi-cation).
mol_align (menu.py:1116-1122) = sele_align (menu.py:1104-1114: to molecule (/CA) ▸, to selection (/CA) ▸, enabled to this, all to this, states (*/CA), states) plus matrix from ▸, matrix to ▸, matrix reset.
modify_sele (menu.py:1124-1133): around ▸ / expand ▸ / extend ▸ / invert ▸ / complete ▸ / restrict ▸ / include ▸ / exclude ▸ — each defined at menu.py:862-986 with fixed distance/bond ladders (4/5/6/8/12/20 Å; 1..6 bonds; plus , residues variants).
copy_to (menu.py:1136-1146, lazy): new + up to 25 enabled objects from cmd.get_object_list('enabled').
move_to_group (menu.py:1148-1158, lazy): new (cmd.group(cmd.get_unused_name(...))), ungroup, then every cmd.get_names_of_type('object:group').

2.2 Show / Hide menus

rep_action(sele, action) (menu.py:145-176) is the shared body used with show / hide / show_as / toggle: wire, lines, nonbonded — licorice, sticks, nb_spheres — ribbon, cartoon — label, cell — dots, spheres — mesh, surface, flag ignore ▸ (set/clear the ignore flag + cmd.rebuild, plus 4 explanatory code 2 note lines).

mol_show (menu.py:197-215): as ▸ (= mol_as, menu.py:178-182, show_as) + rep_action(show) + organic ▸ / main chain ▸ / side chain ▸ / disulfides ▸ (each = show_misc, menu.py:190-195: lines/sticks/spheres) + valence (cmd.set_bond("valence","1",…)).
mol_hide (menu.py:223-240): everything + rep_action(hide) + main chain / side chain / waters / hydrogens ▸ (hide_hydro, menu.py:217-221: all, nonpolar) / unselected / valence.
mol_toggle (menu.py:184-188) — exists but is not wired to any ASHLC button.
measurement_show / measurement_hide (menu.py:243-257): dashes, angles, dihedrals, labels.
cgo_show / cgo_hide (menu.py:259-267): cgo.
simple_show / simple_hide (menu.py:269-275): everything.
map_show / map_hide (menu.py:277-287): dots, extent, everything.
mesh_show / mesh_hide (menu.py:289-299): mesh, cell, everything.
surface_show / surface_hide (menu.py:301-311): surface, cell, everything.
slice_show / slice_hide (menu.py:313-321): slice.
volume_show / volume_hide (menu.py:323-333): volume, extent.

mol_labels (menu.py:1546-1571): clear — residues ("%s-%s"%(resn,resi) anchored on cmd.get("label_anchor")), residues (oneletter), chains, segments — atom name, element symbol, residue name, one letter code, residue identifier, chain identifier, segment identifier — b-factor, occupancy, vdw radius — other properties ▸ (label_props, menu.py:1520-1537: formal charge, partial charge 0.00 / 0.0000, elec. radius, text type, numeric type, stereochemistry) — atom identifiers ▸ (label_ids, menu.py:1539-1544: rank, ID, index).

2.4 Color menus

mol_color (menu.py:672-685): by element ▸ / by chain ▸ / by ss ▸ / by rep ▸ / spectrum ▸ — auto ▸ — then the full colour palette (all_colors).
- by_elem (menu.py:400-418) 8 carbon colours + set 2..set 6/H submenus (by_elem2..by_elem6, menu.py:335-398), all util.cba(<idx>, sele) / util.cbh(<name>, sele); the first entry is util.cnc(sele) (colour non-carbon only).
- by_chain (menu.py:464-480): by chain (elem C) / (*/CA) / all → util.color_chains; chainbows → util.chainbow; by segi (elem C) / by segi → cmd.spectrum("segi","rainbow",…).
- by_ss (menu.py:420-426): 3 preset helix/sheet/loop triples via util.cbss.
- by_rep (menu.py:428-444) over rep_setting_lists (menu.py:482-517): lines→line_color, sticks→stick_color, ribbon→ribbon_color, cartoon→cartoon_color, labels→label_color, dots→dot_color, spheres→sphere_color, mesh→mesh_color, surface→surface_color (mode 1 = measurement: dash/angle/dihedral/label colours; mode 2 = extra 9 settings). Each rep sub-menu = full palette + unset.
- spectrum (menu.py:446-462): rainbow(elem C), rainbow(/CA), rainbow byres, b-factors, b-factors(/CA), area (molecular), area (solvent).
- color_auto (menu.py:659-670): elem C, all, by obj (elem C), by obj.
- all_colors/all_colors_generic (menu.py:625-641): 9 colour groups from all_colors_list (menu.py:519-618) — reds(11), greens(10), blues(9), yellows(7), magentas(10), cyans(7), oranges(7), tints(8), grays(11) — each entry runs cmd.color_deep("<name>", "<sele>", 0); plus a ramps ▸ group listing every object:ramp (colorramps, menu.py:620-623).
general_color (menu.py:711-712): just the palette.
mesh_color (menu.py:696-709): negative ▸ (off + palette writing <rep>_negative_visible / <rep>_negative_color) then the palette. Called with rep="surface" for surface objects.
measurement_color (menu.py:687-694): by rep ▸ (mode 1) + palette.
slice_color (menu.py:655-657): list of ramp objects.
vol_color (menu.py:643-653): panel (cmd.volume_panel) + every named ramp from pymol.colorramping.namedramps.
ramp_color (menu.py:1473-1481): [red, white, blue] + pymol.creating.ramp_spectrum_dict keys → cmd.ramp_update(name, color=…).

2.5 Motion (M button) menus

camera_motion(frame) (menu.py:108-124): store / store with scene ▸ (camera_store_with_scene, first 40 scenes, menu.py:54-59) / store with state ▸ (store_with_state, menu.py:62-80) / clear — reset camera motions — purge entire movie (cmd.mset()) — smooth key frames ▸ (smooth, menu.py:103-106: a little / more (window=15) / a lot (window=30)) — interpolate / reinterpolate / uninterpolate.
obj_motion(obj, frame) (menu.py:126-143): drag — store / store with state ▸ / reset / clear — reset object motions / purge object motions — smooth key frames ▸ — interpolate / reinterpolate / uninterpolate.

2.6 Menus reachable from elsewhere in the viewport (same engine)

main_menu(pos, screenpos) (menu.py:1682-1706) — right-click on empty scene background, invoked at packages/engine/layer1/SceneMouse.cpp:885-886 via MenuActivate3fv: new ▸ (pseudoatom ▸ label / single) — zoom (vis) / orient (vis) / center (vis) / reset — movie ▸ (movie_main, menu.py:1671-1680: play, stop, rewind, panel ▸ on/off) / scene ▸ (scene_main, menu.py:1636-1650: next, append, update, recall ▸ <all scenes>, buttons ▸ on/off) — enable ▸ / disable ▸ (enable_disable, menu.py:1613-1629) — (all) ▸ / (visible) ▸ (all_option, menu.py:1592-1611) — ray — delete all / reinitialize / quit.
pick_menu(title, sele) (menu.py:1782-1798) and pick_sele (menu.py:1709-1733) — right-click on an atom, packages/engine/layer1/SceneMouse.cpp:386-401.
pick_option (menu.py:1735-1779) — the atom/residue/chain/segment/object/molecule/ fragment sub-menus.
seq_option (menu.py:1800-1840) — sequence viewer (other agent’s area, same engine).
scene_menu(name) (menu.py:1842-1849) — right-click a scene button: rename / update / delete.
mouse_config (menu.py:82-101) — right-click the ButMode block: 3-Button Motions / Editing / Viewing / Lights / All Modes, 2-Button Editing / Viewing / Lights.

Behaviours the React menu component must copy:

Geometry: cPopUpLineHeight (item), cPopUpTitleHeight = DIP2PIXEL(19) (code 2), cPopUpBarHeight = DIP2PIXEL(4) (code 0), cPopUpCharWidth = DIP2PIXEL(8) — packages/engine/layer4/PopUp.cpp:40-45, PopUpConvertY packages/engine/layer4/PopUp.cpp:265-....
Placement: initial rect is left = x - Width/3, right = x + 2*Width/3, then PopFitBlock clamps it into the window — packages/engine/layer4/PopUp.cpp:255-261.
Sub-menu opens on hover after cChildDelay = 0.25 s (packages/engine/layer4/PopUp.cpp:47, packages/engine/layer4/PopUp.cpp:527-566) and is placed by PopPlaceChild on whichever side fits (PlacementAffinity).
“Sloppy mousing”: leaving the row keeps the child alive for another cChildDelay; redraws are delayed by cDirtyDelay = 0.05 s; PyMOL_NeedFakeDrag keeps re-entering drag — packages/engine/layer4/PopUp.cpp:585-608, OrthoFakeDrag packages/engine/layer1/Ortho.cpp:305-311.
Click-and-release without dragging inside cPassiveDelay = 0.45 s makes the menu “passive” (sticky — stays open after mouse-up) — packages/engine/layer4/PopUp.cpp:446-465.
Mouse wheel scrolls the whole menu block by 10 px — packages/engine/layer4/PopUp.cpp:436-444.
On commit: PLog then PParse of the command string — packages/engine/layer4/PopUp.cpp:471-475.
Colours flip to black-on-white when internal_gui_mode != Default — packages/engine/layer4/PopUp.cpp:144-163.
Selected row inverts text/background — packages/engine/layer4/PopUp.cpp:866-867; sub-menu rows get left/right gradient “wings” — packages/engine/layer4/PopUp.cpp:884-928.

4. Movie / frame control bar (the Control block)

packages/engine/layer1/Control.cpp. NButton = 9 (packages/engine/layer1/Control.cpp:62), buttons laid out evenly across rect.right - (rect.left + cControlLeftMargin); box size cControlBoxSize = DIP2PIXEL(17) (packages/engine/layer1/Control.cpp:36-42). Icons are only drawn when control_width > 100 (packages/engine/layer1/Control.cpp:655).

#	Icon (draw code)	Action on release (`packages/engine/layer1/Control.cpp:298-376`)	Logged
0	◀ with bar (`:665-696`)	`SceneSetFrame(G,4,0)` — rewind to frame 1	`cmd.rewind()`
1	◀ (`:697-719`)	`SceneSetFrame(G,5,-1)` — step back	`cmd.back()`
2	■ (`:720-742`)	`MoviePlay(cMovieStop)`, also clears `sculpting` and `rock`	`cmd.mstop()`
3	▶ (`:743-761`)	toggle play; with `Ctrl` rewinds first (`cmd.rewind();cmd.mplay()`)	`cmd.mplay()` / `cmd.mstop()`
4	▶ (`:762-785`)	`SceneSetFrame(G,5,1)` — step forward	`cmd.forward()`
5	▶ with bar (`:786-817`)	end; with `Ctrl` → middle	`cmd.ending()` / `cmd.middle()`
6	letter `S` (`:818-822`)	toggle `seq_view`	`cmd.set('seq_view',0\|1)`
7	▼ triangle (`:823-839`)	toggle `rock`, restarts sweep/frame timers	`cmd.rock(0\|1)`
8	letter `F` (`:840-844`)	`full_screen`	`cmd.full_screen()`

“Lit” (ActiveColor {0.65,0.65,0.65}) states: button 6 when seq_view, button 3 when MoviePlaying, button 7 when rock — packages/engine/layer1/Control.cpp:645-649. Pressed state uses {0.8,0.8,0.8} (packages/engine/layer1/Control.cpp:545). Left gutter “nub” (x < rect.left + cControlLeftMargin, packages/engine/layer1/Control.cpp:448-469):

single click + drag horizontally → live-resizes internal_gui_width (min cControlMinWidth = 5) and calls OrthoReshape — packages/engine/layer1/Control.cpp:263-276
double click (<0.35 s) → collapse the panel to width 5 / restore the saved width.

ControlIdling() (packages/engine/layer1/Control.cpp:397-403) — the client must keep animating while sdof active / movie playing / rock / sculpting. ControlSdofButton / ControlSdofUpdate / ControlSdofIterate (packages/engine/layer1/Control.cpp:83-216) implement 6-DOF-device (SpaceNavigator) input — not reproducible in the browser; note as dropped.

5. Movie timeline panel (the Movie block)

packages/engine/layer1/Movie.cpp. Height = MovieGetPanelHeight() packages/engine/layer1/Movie.cpp:1701-1726: movie_panel_row_height (default 15) * ExecutiveCountMotions() rows, or a single row in presentation mode; 0 when movie_panel=0 or there is nothing to show. ExecutiveCountMotions() packages/engine/layer3/Executive.cpp:659-689 counts the camera row (if MovieGetSpecLevel >= 0) plus every object with its own ViewElem. Drawing: CMovie::draw packages/engine/layer1/Movie.cpp:1741-1847.

a horizontal scroll bar spanning the frame range, whose value is the current frame (SceneSetFrame(G,7,value), packages/engine/layer1/Movie.cpp:1770-1783)
ExecutiveMotionDraw packages/engine/layer3/Executive.cpp:694-730 draws one ViewElemDraw strip per row (camera row first, labelled "camera"; object rows labelled with the object name — ObjectDrawViewElem packages/engine/layer1/PyMOLObject.cpp:129-134)
per-frame specification_level: 1 → thin bar (bar_color {0.3,0.3,0.6}), 2 → full-height key block (key_color {0.4,0.4,0.8}) — packages/engine/layer1/View.cpp:158-300
right-hand label gutter LabelIndent = DIP2PIXEL(64) (packages/engine/layer1/Movie.cpp:1865-1867)
when there are no view elems the label is "states" (packages/engine/layer1/Movie.cpp:1841-1843)

Interaction (CMovie::click packages/engine/layer1/Movie.cpp:1488-1568, drag :1574-1607, release :1609-1699):

Input	Effect
Left (no mod)	scrollbar → scrub frame
Left + `Ctrl`	`cMovieDragModeInsDel` → drag right = `cmd.minsert(n, first, object=…)`, drag left = `cmd.mdelete(n, first, object=…)`
Left + `Ctrl+Shift`	same but `DragColumn` (applies to all rows, `object=''`)
Middle + `Ctrl`	`cMovieDragModeOblate` → `cmd.mview('clear', first=…, last=…, object=…)`
Middle + `Ctrl+Shift`	same, column-wide (`object='same'`)
Middle (no mod)	scrollbar
Right	`cMovieDragModeMoveKey` → drag = `cmd.mmove(target, source, 1, object=…)`; click-without-drag opens the motion menu (`ExecutiveMotionMenuActivate`)
Right + `Shift`	`cMovieDragModeCopyKey` → `cmd.mcopy(...)`
Right + `Ctrl+Shift`	`DragColumn`
Wheel	`SceneSetFrame(G,5,±1)` (step frame)
Wheel + `Ctrl+Shift`	change `movie_panel_row_height` and `OrthoReshape`

ExecutiveMotionMenuActivate packages/engine/layer3/Executive.cpp:732-793 picks the row under the cursor and opens camera_motion(frame) for the camera row or obj_motion(objname, frame) for an object row; when DragColumn it uses obj_motion("same", frame). Drag feedback boxes (white outline for source, grey/green/red for target) — packages/engine/layer1/Movie.cpp:1789-1839, ViewElemDrawBox packages/engine/layer1/View.cpp:107-156.

6. Scene bar (in-scene scene buttons)

There is no symbol named MovieButton anywhere in this tree (grepped: no match). The “scene bar” is SceneDrawButtons() packages/engine/layer1/Scene.cpp:2885-3063, drawn by CScene::draw packages/engine/layer1/Scene.cpp:3446-3466 when scene_buttons (default 1, packages/engine/layer1/SettingInfo.h:699) is on. scene_buttons_mode exists but is marked unused (packages/engine/layer1/SettingInfo.h:698).

One button per scene from CScene::SceneVec, stacked bottom-left of the viewport, row height internal_gui_control_size, own scroll bar when the list overflows (packages/engine/layer1/Scene.cpp:2911-2963).
Fill: pressed {0.7,0.7,0.7}; current scene (name == scene_current_name) {0.5,0.5,0.5}; otherwise {0.25,0.25,0.25} — packages/engine/layer1/Scene.cpp:3029-3038.
ButtonMargin is exported so the scene image is not overlapped (packages/engine/layer1/Scene.cpp:3024-3025).

Interaction — SceneClickSceneButton packages/engine/layer1/SceneMouse.cpp:179-221 and SceneRelease packages/engine/layer1/SceneMouse.cpp:1070-1140, SceneDrag :1233-1305:

Input	Effect
Left click	`PressMode 1` → on release `cmd.scene('<name>')` (with interpolation)
Middle click	`PressMode 2` → immediate `cmd.scene('<name>', animate=-1)`; with `Ctrl`, `animate=0`
Right click	`PressMode 3` → drag reorders (`cmd.scene_order([...])`, `location='top'` when dropped on the first slot); click-without-drag opens `scene_menu(name)` (passive)

7. Mouse-mode block (ButMode)

packages/engine/layer1/ButMode.cpp:192-395. Text-only block:

line 1: "Mouse Mode " + button_mode_name (colour {1,0.5,0.5}).
if mouse_grid (default 1, packages/engine/layer1/SettingInfo.h:687): a 4×(3+wheel) matrix — header Buttons / L M R Wheel, then rows & Keys, Shft, Ctrl, CtSh, then SnglClk and DblClk rows. Cell contents are 5-char codes from CButMode::Code, initialised at packages/engine/layer1/ButMode.cpp:497-520+: Rota , RotZ , Move , MovZ , Clip , ClpN , ClpF , PkAt , PkBd , TorF , RotF , MovF , lb , mb , rb , +lb , +mb , +rb , Orig , +lBx , -lBx , … (blank = " ").
last lines: Picking Atoms (and Joints) or Selecting <Atoms|Residues|Chains|Segments|Objects|Molecules|C-alphas> from mouse_selection_mode — packages/engine/layer1/ButMode.cpp:355-390.
fast-redraw line: Frame/State %4d/%4d plus %5.1f Hz when show_frame_rate (packages/engine/layer1/ButMode.cpp:423-475).

Click (packages/engine/layer1/ButMode.cpp:149-190):

in the bottom 2 lines (dy < 2) → cycle the selection mode: mouse select_forward / mouse select_backward (reversed by right button, wheel-back, or Shift)
elsewhere: left/wheel → mouse forward / mouse backward; right button → opens the mouse_config popup.

8. Wizard block

packages/engine/layer1/Wizard.cpp. WizardRefresh() packages/engine/layer1/Wizard.cpp:195-259 pulls wizard.get_prompt() (a list of strings → the floating wizard prompt) and wizard.get_panel() (list of [type, text, code]) and resizes the block to internal_gui_control_size * NLine + 4. Line types (packages/engine/layer1/Wizard.cpp:45-47): 1 = text, 2 = button, 3 = popup.

click on a button → pressed state; on release PParse(code) — packages/engine/layer1/Wizard.cpp:481-580
click on a popup line → wizard.get_menu(code) → PopUpNew — packages/engine/layer1/Wizard.cpp:495-513
drag highlights the button under the cursor — packages/engine/layer1/Wizard.cpp:519-550
event mask get_event_mask() (cWizEventPick + cWizEventSelect default) — packages/engine/layer1/Wizard.cpp:213-221

Wizard prompt overlay (independent of the block): OrthoDrawWizardPrompt() packages/engine/layer1/Ortho.cpp:2124-2255. wizard_prompt_mode (default 1, packages/engine/layer1/SettingInfo.h:461): 1 = filled box top-left, 2 = text only, 3 = flush to the very top-left corner. Text may carry \RGB colour codes. Position accounts for the sequence viewer height when seq_view_location=0.

9. Command prompt drawn inside the viewport

State lives in COrtho (packages/engine/layer1/Ortho.cpp:68-149): a Line[256] ring of scrollback lines (OrthoSaveLines 0xFF), a History[256] ring (OrthoHistoryLines 0xFF), CurLine, CurChar, PromptChar, CursorChar, InputFlag, Prompt[255], Saved/SavedPC/SavedCC (the in-progress line stashed while output is written).

9.1 Key handling — `OrthoKey()` `packages/engine/layer1/Ortho.cpp:841-1031`

Key / chord	Behaviour
any printable >32, ≠127	insert at cursor (`add_normal_char`, `packages/engine/layer1/Ortho.cpp:822-839`)
`mod == 4` (Alt)	`cmd._alt(chr(k))`; `Alt+@` is treated as plain `@` — `packages/engine/layer1/Ortho.cpp:803-820`
`mod == 3` (Ctrl+Shift)	`cmd._ctsh(chr(k+64))` — `packages/engine/layer1/Ortho.cpp:789-801`
other Ctrl chars (default branch)	`cmd._ctrl(chr(k+64))` — `packages/engine/layer1/Ortho.cpp:761-773`, `:1024-1026`
Space, empty line	`mtoggle` (or, in `presentation`, `cmd.scene('','next')`); `Shift+Space` → `rewind;mplay` — `packages/engine/layer1/Ortho.cpp:876-893`
Space, non-empty line	insert a space
Backspace (8)	delete left of cursor, never past `PromptChar`
Delete (127)	delete right of cursor; on an empty line falls through to `Ctrl-D`
Ctrl-A (1)	cursor to start of input
Ctrl-E (5)	cursor to end
Ctrl-D (4)	delete forward, or (empty line) filename/keyword completion print only via `PComplete`
Tab (9)	`PComplete` and replace the line
Ctrl-K (11)	truncate line at cursor
Ctrl-V (22)	`cmd.paste()` when the line is empty-ish
Enter (13), non-empty	`OrthoParseCurrentLine()` — push to history, `PLog` (except `quit`), `PParse` — `packages/engine/layer1/Ortho.cpp:1033-1060`
Enter (13), empty, movie panel or presentation and a movie exists	`mview toggle,quiet=1`; `+Ctrl` → `mview toggle,freeze=1`; `+Shift` → `mview toggle_interp`; `+Ctrl+Shift` → `mview toggle_interp,object=same`; in `presentation` plain Enter → `mtoggle` — `packages/engine/layer1/Ortho.cpp:961-983`
Esc (27)	dismiss splash; else toggle `text`; `Shift+Esc` toggles `overlay`; in `presentation` → `_quit` — `packages/engine/layer1/Ortho.cpp:941-959`

OrthoSpecial() packages/engine/layer1/Ortho.cpp:322-389 handles ↑/↓ (history recall, saving the in-progress line back into History[HistoryLine]) and ←/→ (cursor). Arrows are only grabbed when OrthoArrowsGrabbed() — i.e. there is typed text and text is visible (packages/engine/layer1/Ortho.cpp:394-409); otherwise they fall through to _special → packages/engine/modules/pymol/shortcut_dict.py bindings (packages/engine/layer5/PyMOL.cpp:2361-2395).

9.2 Feedback / scrollback rendering

OrthoDrawText() packages/engine/layer1/Ortho.cpp:1623-1693:

origin x = cOrthoLeftMargin, y = cOrthoBottomMargin + MovieGetPanelHeight(G)
number of lines: ShowLines (= height/cOrthoLineHeight) when text is on or the splash is up, otherwise internal_feedback + overlay_lines
internal_prompt = 0 hides the prompt line entirely (skip_prompt, packages/engine/layer1/Ortho.cpp:1633-1634)
the input line gets a _ cursor glyph, positioned at CursorChar when set (packages/engine/layer1/Ortho.cpp:1676-1685)
colour: prompt lines use TextColor, output lines use OverlayColor (= 1 − background, zeroed if too close to the background, packages/engine/layer1/Ortho.cpp:1874-1880)
background strip: OrthoDrawInternalFeedbackBG() packages/engine/layer1/Ortho.cpp:1506-1553 (black band across the bottom under the scene plus a {0.3,0.3,0.3} separator line)

Overlay-line count: OrthoGetNumberOverlayLines() packages/engine/layer1/Ortho.cpp:1591-1621. overlay (default 0, packages/engine/layer1/SettingInfo.h:145), overlay_lines (default 5, packages/engine/layer1/SettingInfo.h:400), auto_overlay (default 0, packages/engine/layer1/SettingInfo.h:703) makes new output transiently visible until OrthoRemoveAutoOverlay() (packages/engine/layer1/Ortho.cpp:426-431, called on every mouse click, packages/engine/layer1/Ortho.cpp:2528). Line assembly: OrthoAddOutput() packages/engine/layer1/Ortho.cpp:1062-1127 (wraps at wrap_output columns, default 0 = off, packages/engine/layer1/SettingInfo.h:276), OrthoNewLine() packages/engine/layer1/Ortho.cpp:1129-1189 (also pushes the line into the feedback queue and strips ANSI escapes unless colored_feedback, packages/engine/layer1/SettingInfo.h:874). Queue drain for an external GUI: OrthoFeedbackOut() packages/engine/layer1/Ortho.cpp:502-516 → _cmd.get_feedback (packages/engine/layer4/Cmd.cpp:3866-3900) → cmd._get_feedback() (packages/engine/modules/pymol/internal.py:593-606). The Qt GUI polls it every 500 ms and converts to HTML with colorprinting.text2html — packages/engine/modules/pmg_qt/pymol_qt_gui.py:941-957. Command input from an external GUI goes the other way through OrthoCommandIn() / OrthoCommandOut() (packages/engine/layer1/Ortho.cpp:2851-2868, :455-470) with a 4-deep nesting stack (OrthoCommandNest, packages/engine/layer1/Ortho.cpp:440-453).

10. Busy / progress box and splash

OrthoBusyDraw() packages/engine/layer1/Ortho.cpp:609-724 — a 240×60 px black box in the top-left with a message line and up to two progress bars (BusyStatus[0..3] = slow progress/total, fast progress/total), gated by show_progress. Fed by OrthoBusySlow / OrthoBusyFast (packages/engine/layer1/Ortho.cpp:538-596) which also call PyMOL_SetProgress. Python side: cmd.get_progress() (packages/engine/modules/pymol/monitoring.py:5), already consumed by the Qt GUI at packages/engine/modules/pmg_qt/pymol_qt_gui.py:931-939.
OrthoSplash() packages/engine/layer1/Ortho.cpp:2608-2679 — version/copyright text; SplashFlag forces full text display until the first click (OrthoRemoveSplash, packages/engine/layer1/Ortho.cpp:433-438, called from OrthoButton packages/engine/layer1/Ortho.cpp:2527).
OrthoDrawLoop() packages/engine/layer1/Ortho.cpp:1695-1750 — the 1-px rubber-band selection rectangle (LoopRect, set via OrthoSetLoopRect packages/engine/layer1/Ortho.cpp:253-261), coloured cColorFront.
OrthoDrawMessages() packages/engine/layer1/Ortho.cpp:1752-1781 — build-flavour banners (PYMOL_EVAL, PYMOL_EDU, …); not applicable to this fork’s default build.

11. Reading the panel state from Python (confirmed APIs)

All of the following were verified to exist in this tree.

Need	API	Source
Row names, in SpecRec order	`cmd.get_names(type, enabled_only, selection)` with `type` ∈ objects / selections / all / public / public_objects / public_selections / public_nongroup_objects / public_group_objects / nongroup_objects / group_objects	`packages/engine/modules/pymol/querying.py:1155-1199`; C: `ExecutiveGetNames` `packages/engine/layer3/Executive.cpp:8873-8960`
Row kind	`cmd.get_type(name)` → `object:molecule`, `object:map`, `object:mesh`, `object:slice`, `object:surface`, `object:measurement`, `object:cgo`, `object:group`, `object:volume`, `selection`	`packages/engine/modules/pymol/querying.py:1206-1240`
All names of one kind	`cmd.get_names_of_type('object:group')`	`packages/engine/modules/pymol/querying.py:1459-1485`
enabled + reps + colour, all rows at once	`cmd.get_vis()` → `{name: [visible:int, [], [rep_indices] \| None, color_index \| None]}`	`packages/engine/modules/pymol/viewing.py:899-901`; C: `ExecutiveGetVisAsPyDict` `packages/engine/layer3/Executive.cpp:4496-4527` (rep list built by `getRepArrayFromBitmask` `:4529-4540`; `_`-prefixed recs are skipped)
Restore that state	`cmd.set_vis(dict)`	`packages/engine/modules/pymol/viewing.py:903-905`; C: `ExecutiveSetVisFromPyDict` `packages/engine/layer3/Executive.cpp:4574`
Enabled-only listing	`cmd.get_names('objects', enabled_only=1)`	used by `menu.enable_disable` `packages/engine/modules/pymol/menu.py:1613-1629`
Object colour index	`cmd.get_object_color_index(name)`	`packages/engine/modules/pymol/querying.py:819-823`
Colour index → RGB	`cmd.get_color_tuple(name_or_index)`	`packages/engine/modules/pymol/querying.py:825-841`
Atom count for a row/selection	`cmd.count_atoms(selection)`	`packages/engine/modules/pymol/querying.py:1419-1441`
State count / caption numbers	`cmd.count_states(selection)`, `cmd.get_title(object, state)`	`packages/engine/modules/pymol/querying.py:703`, `:176`
Objects covered by a selection	`cmd.get_object_list(selection)`	`packages/engine/modules/pymol/querying.py:131-145`
Frame / state / movie	`cmd.get_frame()`, `cmd.get_state()`, `cmd.count_frames()`, `cmd.get_movie_length()`, `cmd.get_movie_playing()`, `cmd.get_movie_locked()`	`packages/engine/modules/pymol/moving.py:984`, `:958`, `packages/engine/modules/pymol/querying.py:759`, `:730`, `packages/engine/modules/pymol/moving.py:64`, `packages/engine/modules/pymol/querying.py:814`
Scene bar contents / order	`cmd.get_scene_list()` (→ `_cmd.get_scene_order`), `cmd.scene_order(...)`, `cmd.get_scene_message`	`packages/engine/modules/pymol/viewing.py:919-921`, `:961`, `:935`
Feedback stream	`cmd._get_feedback()`	`packages/engine/modules/pymol/internal.py:593-606`
Progress	`cmd.get_progress()`	`packages/engine/modules/pymol/monitoring.py:5`
Settings that changed since last poll	`cmd.get_setting_updates()`	`packages/engine/modules/pymol/setting.py:440`
Tab completion for the prompt	`cmd._parser.complete(str)` (exposed as `new_complete_closure`)	`packages/engine/modules/pymol/parser.py:524-604`
Menu contents (do NOT re-implement)	`pymol.menu.<name>(cmd, *args)` — returns the `[code, text, command]` list; entries whose 3rd element is a callable must be called with no args to expand	`packages/engine/modules/pymol/menu.py`, mirrors `packages/engine/layer4/Menu.cpp:29-124` and `packages/engine/layer4/PopUp.cpp:88-110`

Gaps in the Python surface (confirmed by grep, not guessed)

Group nesting / indent level and group open-closed state are NOT exposed by any cmd.* query. PanelRec.nest_level / is_open live only in C (packages/engine/layer3/ExecutiveDef.h:20-31) and SpecRec::group_name is only serialised through cmd.get_session(partial=1)['names'] — element 6 of each rec is group_name (ExecutiveGetExecObjectAsPyList packages/engine/layer3/Executive.cpp:5377-5448, ExecutiveGetExecSeleAsPyList :5450-5468), and ObjectGroup.OpenOrClosed is element 1 of the group’s own list (ObjectGroupAsPyList packages/engine/layer2/ObjectGroup.cpp:60-73). cmd.get_session is far too heavy to poll, so the bridge supplies the panel model itself in packages/bridge/tenmol_bridge/panels/objects.py rather than reading PanelRec.
There is no push notification for panel changes in the Python build: ReportEnabledChange (packages/engine/layer3/Executive.cpp:313-326) only invokes G->enabledCallback under _PYMOL_LIB. The fork bumps m_web_enable_version at the top of that same function (:315-319), which is what _cmd.web_get_versions reports, so the client polls four counters instead of diffing names.
sele_color (per-selection indicator colour) is in SpecRec but has no cmd getter.
cmd.get_vis() reports visible per rec but not the “cloaked” state (enabled but an ancestor group is disabled); that has to be derived client-side from group membership, matching packages/engine/layer3/Executive.cpp:16443-16461.

12. Consequences for the port

Menus are fetched from the backend as data (pymol.menu.* → JSON), not re-declared in TypeScript: the entries embed cmd.* source strings and are generated from live state (scene lists, ramp lists, object lists, colour list). Each selected leaf is executed via cmd.do(<command string>) — which is exactly what packages/engine/layer4/PopUp.cpp:471-475 does (PLog + PParse). See apps/web/src/features/pymol-menu/menuStore.ts.
Lazy sub-menus (lambda: copy_to(...), lambda: move_to_group(...), menu.py:1182, :1208, :1235, :1269-1270, :1299, :1315, :1402, :1438, :1455, :1468, :1740, :1776) are expanded on demand, mirroring SubGetItem packages/engine/layer4/PopUp.cpp:88-110.
Text colour codes \RGB are parsed into spans (packages/engine/layer1/Text.cpp:507-548, ported in apps/web/src/features/wizards/colorCodes.ts); they appear in menu labels (del_col/rem_col = \933, menu.py:21-22), object captions, and wizard prompts.
The panel is the only place where drag-reorder/regroup exists; it emits real cmd.order / group / ungroup commands, so the tree can be optimistic and then re-read (apps/web/src/features/objects/placement.ts).
Modifier semantics (Shift/Ctrl/Ctrl+Shift on left and middle mouse over a row) are non-obvious and are part of the product; see §1.4.

Overview

Packages

Area maps

Spikes

API reference

Internal GUI (the panels PyMOL draws inside the viewport)

Internal GUI (the panels PyMOL draws inside the viewport)

0. Layout model

1. Object panel (“names list”, the Executive block)

1.1 Row model

1.2 What a row draws (left→right)

1.3 Click semantics on the toggle buttons

1.4 Click semantics on the name / group control

1.5 Panel-level behaviours

2.1 Action menus

2.2 Show / Hide menus

2.3 Label menu

2.4 Color menus

2.5 Motion (M button) menus

2.6 Menus reachable from elsewhere in the viewport (same engine)

4. Movie / frame control bar (the Control block)

5. Movie timeline panel (the Movie block)

6. Scene bar (in-scene scene buttons)

7. Mouse-mode block (ButMode)

8. Wizard block

9. Command prompt drawn inside the viewport

9.1 Key handling — `OrthoKey()` `packages/engine/layer1/Ortho.cpp:841-1031`

9.2 Feedback / scrollback rendering

10. Busy / progress box and splash

11. Reading the panel state from Python (confirmed APIs)

Gaps in the Python surface (confirmed by grep, not guessed)

12. Consequences for the port

​Internal GUI (the panels PyMOL draws inside the viewport)

​0. Layout model

​1. Object panel (“names list”, the Executive block)

​1.1 Row model

​1.2 What a row draws (left→right)

​1.3 Click semantics on the toggle buttons

​1.4 Click semantics on the name / group control

​1.5 Panel-level behaviours

​2. The popup menus (contents)

​2.1 Action menus

​2.2 Show / Hide menus

​2.3 Label menu

​2.4 Color menus

​2.5 Motion (M button) menus

​2.6 Menus reachable from elsewhere in the viewport (same engine)

​3. Popup-menu engine (packages/engine/layer4/PopUp.cpp)

​4. Movie / frame control bar (the Control block)

​5. Movie timeline panel (the Movie block)

​6. Scene bar (in-scene scene buttons)

​7. Mouse-mode block (ButMode)

​8. Wizard block

​9. Command prompt drawn inside the viewport

​9.1 Key handling — OrthoKey() packages/engine/layer1/Ortho.cpp:841-1031

​9.2 Feedback / scrollback rendering

​10. Busy / progress box and splash

​11. Reading the panel state from Python (confirmed APIs)

​Gaps in the Python surface (confirmed by grep, not guessed)

​12. Consequences for the port

Internal GUI (the panels PyMOL draws inside the viewport)

0. Layout model

1. Object panel (“names list”, the Executive block)

1.1 Row model

1.2 What a row draws (left→right)

1.3 Click semantics on the toggle buttons

1.4 Click semantics on the name / group control

1.5 Panel-level behaviours

2. The popup menus (contents)

2.1 Action menus

2.2 Show / Hide menus

2.3 Label menu

2.4 Color menus

2.5 Motion (M button) menus

2.6 Menus reachable from elsewhere in the viewport (same engine)

3. Popup-menu engine (`packages/engine/layer4/PopUp.cpp`)

4. Movie / frame control bar (the Control block)

5. Movie timeline panel (the Movie block)

6. Scene bar (in-scene scene buttons)

7. Mouse-mode block (ButMode)

8. Wizard block

9. Command prompt drawn inside the viewport

9.1 Key handling — `OrthoKey()` `packages/engine/layer1/Ortho.cpp:841-1031`

9.2 Feedback / scrollback rendering

10. Busy / progress box and splash

11. Reading the panel state from Python (confirmed APIs)

Gaps in the Python surface (confirmed by grep, not guessed)

12. Consequences for the port