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Settings and colors

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PART A — THE SETTINGS SYSTEM

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A1. The setting table is a static C table, generated twice from one header

• 798 total records; index range 0 .. 797; cSetting_INIT = 798 (packages/engine/layer1/SettingInfo.h:913).
• By type: 219 boolean, 203 int, 294 float, 15 float3, 34 color, 32 string, 1 blank (REC__( 83, ) at packages/engine/layer1/SettingInfo.h:167).
• By level: 454 global, 231 object-state (ostate), 44 object, 27 atom, 17 atom-state (astate), 6 bond, 18 unused (+1 blank).
• 779 settings are visible to Python. SettingGetSettingIndices() (packages/engine/layer1/Setting.cpp:3227-3245) skips every record whose level is cSettingLevel_unused, so the 18 retired settings + 1 blank never appear in index_dict.
• packages/engine/modules/pymol/setting.py:48 then injects one legacy alias, ray_shadows -> ray_shadow, into index_dict after name_list was captured at setting.py:44. Net effect: len(setting.get_name_list()) == 779, len(setting.index_dict) == 780.
• Indices are frozen forever (they are serialized into .pse sessions) — packages/engine/layer1/SettingInfo.h:5-6 “WARNING: do not delete or change indices”; regression-tested at packages/engine/testing/tests/api/setting.py:5-8 (collada_geometry_mode == 742).
• The last three added settings are 795 salt_bridge_distance, 796 use_tessellation_shaders, 797 cell_color (packages/engine/layer1/SettingInfo.h:895-908).

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A2. Levels form a non-linear lattice

{"unused",0x00} {"global",0x00} {"object",0x01} {"object-state",0x03}
{"atom",0x07} {"atom-state",0x0F} {"bond",0x13} {"bond-state",0x33}

• SettingLevelGetName(index) → level name string (packages/engine/layer1/Setting.cpp:83-85).
• SettingLevelCheckMask / SettingLevelCheck (packages/engine/layer1/Setting.cpp:88-96) validate that a setting may be written at a requested level.
• Writing at a wrong level is a warning, not an error: packages/engine/layer3/Executive.cpp:12279-12286 prints " Setting-Warning: '%s' is a %s-level setting" and still performs the write (which then silently has no effect). packages/engine/modules/pymol/setting.py:230-247 documents the per-atom whitelist and setting.py:148-155 the per-bond whitelist as prose only.
• alter/alter_state enforce hard: packages/engine/layer1/P.cpp:523-528 (astate) and P.cpp:531-536 (atom) raise TypeError.

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A3. Runtime introspection surface exposed to Python

• boolean: any float parses; non-zero → 1; otherwise boolean_dict (setting.py:50-59) accepts true/false/on/off/1/0/1.0/0.0 with Shortcut abbreviation.
• int/float: strings that look boolean are converted first, then int()/float().
• float3: list/tuple passthrough; string with commas goes through cmd.safe_eval (packages/engine/modules/pymol/constants.py:106-117), otherwise whitespace split; always returns 3 floats.
• color: str(value) — resolution happens in C (SettingSet_color, packages/engine/layer1/Setting.cpp:1740-1770).
• string: outermost matching quotes stripped.

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A4. Read/write semantics

• boolean/int/color → (type, int)
• float → (type, float) via pretty_f2d (7 significant digits, packages/engine/testing/tests/api/setting.py:49-55)
• float3 → (type, (f,f,f))
• string → (type, str)
• blank → None

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A5. Change notification — get_setting_updates is destructive and single-consumer

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A6. Atom-, atom-state- and bond-level settings

• s[key] read — packages/engine/layer1/P.cpp:455-486. Key may be an int index or a name string (get_and_check_setting_index, P.cpp:425-443, raises LookupError for unknown). Lookup cascade: atom-state → atom → object-state/object/global.
• s[key] = v write — packages/engine/layer1/P.cpp:502-539; read-only outside alter/alter_state (P.cpp:512-516), and level-checked as noted in A2.
• iter(s) — packages/engine/layer1/P.cpp:581-606 → SettingUniqueGetIndicesAsPyList (packages/engine/layer1/Setting.cpp:3249-3268): yields the indices actually defined on that atom/atom-state. This is the only way to enumerate per-atom overrides, and it returns numbers, not names.
• Storage is the CSettingUnique sparse map keyed by unique_id (packages/engine/layer1/Setting.h:34-50; packages/engine/layer2/AtomInfo.cpp:74-95; packages/engine/layer2/CoordSet.cpp:1704-1719).
• Bond level is read back via cmd.get_bond (packages/engine/modules/pymol/setting.py:449-514, C at packages/engine/layer3/Executive.cpp:11843, level gate at Executive.cpp:11969).
• unset_deep docstring (packages/engine/modules/pymol/setting.py:519-526) documents the escape hatch for atom-state settings: alter_state 1, *, del s[728] (728 = label_screen_point).

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A7. Session / defaults lifecycle

• Blacklist for .pse persistence — packages/engine/layer1/Setting.cpp:627-660: unused-level plus antialias_shader, ati_bugs, cache_max, cgo_shader_ub_*, colored_feedback, cylinder_shader_ff_workaround, defer_updates, fast_idle, fetch_path, internal_feedback, internal_gui, internal_prompt, logging, max_threads, mouse_grid, mouse_scale, nb_spheres_use_shader, no_idle, nvidia_bugs, presentation, precomputed_lighting, render_as_cylinders, security, session_changed, session_file, …. Used by SettingAsPyList (Setting.cpp:956-975) and SettingFromPyList (Setting.cpp:1024).
• SettingInitGlobal (packages/engine/layer1/Setting.cpp, after line 1180) resets from SettingInfo, honours reset_gui (skips internal_gui, internal_gui_width), forces volume_mode=0 in open source, and applies command-line overrides (auto_show_lines/spheres/nonbonded, auto_zoom, presentation, defer_builds_mode, presentation_auto_quit, internal_feedback, stereo_mode).
• cmd.reinitialize(what) with reinit_code (packages/engine/modules/pymol/commanding.py:350-356): everything=0, settings=1, store_defaults=2, original_settings=3, purge_defaults=4. Surfaced in the File menu (packages/engine/modules/pymol/_gui.py:128-131).
• SettingStoreDefault / SettingPurgeDefault / SettingRestoreDefault (packages/engine/layer1/Setting.h:161-162, packages/engine/layer1/Setting.cpp:1528-1573).

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PART B — THE QT SETTING UI (what becomes React)

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B1. Menu data is toolkit-independent already

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B2. Full enumeration — the Setting menu (packages/engine/modules/pymol/_gui.py:492-773)

• Edit All… → settings_edit_all_dialog (advanced table, B4)
• Keyboard Shortcuts… → shortcut_menu_edit_dialog
• Colors… → edit_colors_dialog (B10)
• separator

• Size radios on label_size: 10/14/18/24/36/48/72 Point; separator; 0.3/0.5/1/2/4 Angstrom (negated values)
• Font radios on label_font_id: Sans 5, Sans Oblique 6, Sans Bold 7, Sans Bold Oblique 8, Serif 9, Serif Oblique 17, Serif Bold 10, Serif Bold Oblique 18, Mono 11, Mono Oblique 12, Mono Bold 13, Mono Bold Oblique 14, Gentium Roman 15, Gentium Italic 16
• Color radios on label_color: Front −6, Back −7
• check Show Connectors → label_connector
• Background Color radios on label_bg_color: None −1, Back −7, Front −6

• check Ball and Stick → stick_ball 1
• Ball and Stick Ratio radios stick_ball_ratio: 1.0, 1.5, VDW (−1.0)
• Zero Order Bonds radios valence_zero_mode: Hide 0, Dashed 1, Solid 2
• Zero Order Stick Scale radios valence_zero_scale: 0.1, 0.2, 0.3, 1.0
• Stick Radius radios stick_radius: .1, .2, .25
• Stick Hydrogen Scale radios stick_h_scale: .4, 1.
• Line Width radios line_width: 1.0, 1.49, 3.0
• check Lines As Cylinders → line_as_cylinders 1

• Rings and Bases: cartoon_ring_mode 1/2/3/4/0 (Filled Round / Filled Flat / Filled with Border / Spheres / Base Ladders); cartoon_ring_finder 1/2/3/4 (Bases and Sugars / Bases Only / Non-protein Rings / All Rings); cartoon_ring_transparency 0.5 / −1
• checks: Side Chain Helper cartoon_side_chain_helper, Round Helices cartoon_round_helices, Fancy Helices cartoon_fancy_helices, Cylindrical Helices cartoon_cylindrical_helices, Flat Sheets cartoon_flat_sheets, Fancy Sheets cartoon_fancy_sheets, Smooth Loops cartoon_smooth_loops, Discrete Colors cartoon_discrete_colors, Highlight Color cartoon_highlight_color on=104 off=−1
• Sampling radios cartoon_sampling: −1 (Atom count dependent), 2, 7, 14
• Gap Cutoff radios cartoon_gap_cutoff: 0, 5, 10, 20

• checks ribbon_side_chain_helper, ribbon_trace_atoms
• radios ribbon_as_cylinders 0 (As Lines) / 1 (As Cylinders)
• Cylinder Radius radios ribbon_radius: 0. (Match Line Width), .2, .5, 1. Angstrom

• Color radios surface_color: White 0, Light Gray 4236, Gray 25, Default (Atomic) −1
• radios surface_type: Dot 1, Wireframe 2, Solid 0
• radios surface_cavity_mode: 1 Cavities and Pockets Only, 2 Culled, 0 Exterior (Normal)
• Cavity Detection Radius radios surface_cavity_radius: 7 Angstrom; −3,−4,−5,−6,−8,−10,−20 Solvent Radii
• Cavity Detection Cutoff radios surface_cavity_cutoff: −1..−5 Solvent Radii
• check Solvent Accessible surface_solvent
• checks Smooth Edges surface_smooth_edges, Edge Proximity surface_proximity
• radios surface_mode: Ignore None 1, Ignore HETATMs 0, Ignore Hydrogens 2, Ignore Unsurfaced 3

• check Pre-integrated Rendering volume_mode
• Number of Layers radios volume_layers: 100, 256, 500, 1000

• four submenus from transparency_menu() (_gui.py:66-71) on transparency, sphere_transparency, cartoon_transparency, stick_transparency, each radios Off 0.0 / 20% / 40% / 50% / 60% / 80%
• composite commands setting (transparency_mode, backface_cull, two_sided_lighting): Uni-Layer (2,1,0), Multi-Layer (1,0,1), Multi-Layer (Real-time OIT) (3,0,−1), Fast and Ugly (0,1,0)
• check Angle-dependent ray_transparency_oblique 1.0

• check OpenGL 2.0 Shaders use_shaders
• check Antialias (Ray Tracing) antialias
• Antialias (Real Time) radios antialias_shader: off 0, FXAA 1, SMAA 2
• command Modernize → cmd.util.modernize_rendering(1, cmd) (packages/engine/modules/pymol/util.py:553)
• Shadows: 9 commands → cmd.util.ray_shadows(v) (packages/engine/modules/pymol/util.py:821) for none/light/medium/heavy/black, then matte/soft/occlusion/occlusion2
• Texture radios ray_texture: None 0, Matte 1 = 1, Matte 2 = 4, Swirl 1 = 2, Swirl 2 = 3, Fiber 5
• Interior Texture radios ray_interior_texture: same 6 values
• Memory radios hash_max: 70 / 100 / 170 / 230 / 300
• check Cull Backfaces backface_cull
• check Opaque Interiors ray_interior_color on=74 off=−1

• PDB File Loading: check ignore_pdb_segi
• mmCIF File Loading: check cif_use_auth; check Load Assembly assembly on=“1” off="" (a string setting used as a toggle); check Bonding by CCD connect_mode on=4 off=0
• Map File Loading: checks normalize_ccp4_maps, normalize_o_maps

• check Cartoon/Sticks/Spheres by Classification auto_show_classified on=−1 off=0
• checks auto_show_lines, auto_show_spheres, auto_show_nonbonded
• checks auto_show_selections, auto_hide_selections

• check Auto-Zoom New Objects auto_zoom
• check Auto-Remove Hydrogens auto_remove_hydrogens
• check Show Text (Esc) text
• check Overlay Text overlay

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B3. Settings that also live in the Display menu (packages/engine/modules/pymol/_gui.py:377-491)

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B4. Advanced settings table (packages/engine/modules/pmg_qt/advanced_settings_gui.py)

• QLineEdit placeholder “Filter” wired to QSortFilterProxyModel.setFilterRegularExpression (lines 25-28) — the filter is a regex over both columns.
• populateData() (40-67): sorted(setting.get_name_list()) → 779 rows; per row setting._get_index(name) then cmd.get_setting_tuple(index).
  • type 1 (bool) → checkable item, not text-editable
  • types 2, 6 (int, str) → str(v_list[0])
  • types 3, 4, 5 (float, float3, color) → cmd.get(index) i.e. the text form
  • name column is read-only (Qt.ItemIsEnabled only)
  • setting index stashed in value_item.setData(index)
• formatTable() (69-80): headers hidden both axes, last column stretches, columns auto-resized.
• itemChanged (82-99): checkbox → cmd.set(index, checked, log=1, quiet=0); else cmd.set(index, item.text(), log=1, quiet=0).
• Known gaps to fix in the port: no level column, no default value, no min/max validation, no reset/unset action, no help text, no per-object scope, no live refresh from get_setting_updates (the table goes stale when a menu changes a setting), and edits are swallowed on error because cmd.set failures are not surfaced.

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B5. Lighting Settings plugin (packages/engine/data/startup/lightingsettings_gui/main.py)

• SettingSlider(QSlider) (main.py:13-61): integer slider mapped onto a float range with resolution res, paired QLineEdit, writes on every valueChanged via cmd.set(self.setting, self.getDoubleValue()), objectName = setting name so update_setting() can find and refresh it (main.py:64-68).
• Presets (main.py:70-139): Default, Metal, Plastic, Rubber, X-Ray — each a fixed list of cmd.set calls over ambient, direct, spec_direct, spec_direct_power, light_count, shininess, reflect, spec_count, spec_power, spec_reflect, specular, specular_intensity, ambient_occlusion_mode, ambient_occlusion_scale, ambient_occlusion_smooth, power, reflect_power.
• Slider layout with section headers (main.py:157-188): Diffuse Reflection (ambient 0–1, reflect −1–1); Direct Light from Front (direct −1–1, spec_direct 0–1, spec_direct_power 0–100 step 1); Free placeable directed Lights (light_count 1–8, edit_light 1–7); Specular Reflection (spec_count −1–8, shininess 0–100, spec_reflect −0.01–1, specular 0–1, specular_intensity 0–1); Ambient Occlusion (Surface only) (ambient_occlusion_mode 0–2, ambient_occlusion_scale 1–50, ambient_occlusion_smooth 1–20); Ray trace only (power 1–10, reflect_power 1–10).
• Note spec_power is commented out as deprecated since v1.5 (main.py:174).

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PART C — THE COLOR SYSTEM

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C1. The color table: 5388 slots, index layout is load-bearing

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C2. Special / encoded color indices

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C3. Python color API

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C4. Palettes and spectrum

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C5. Color ramps (ramp objects) and volume ramps

• Ramps are real objects (object:ramp) registered as color “extensions”: ColorRegisterExt (packages/engine/layer1/Color.cpp:347-365), ColorForgetExt (Color.cpp:367), ColorRenameExt (Color.cpp:1894). Their color index is -10 - ext_slot.
• ColorCheckRamped (Color.cpp:168-171), ColorGetRamp (Color.cpp:173-187), ColorGetRamped (Color.cpp:189-218) — a ramped color is evaluated per vertex (vertex, state), which is why ramp-colored geometry must be baked server-side before it reaches three.js.
• cmd.ramp_new(name, map_name, range, color, state, selection, beyond, within, sigma, zero, quiet) — packages/engine/modules/pymol/creating.py:374-490. color may be a list of names/tuples (each resolved with get_color_tuple(a, 4) so specials survive) or one of the named spectra in ramp_spectrum_dict (creating.py:47-57): traditional 1, sludge 2, ocean 3, hot 4, grayable 5, rainbow 6, afmhot 7, grayscale 8, object [[-1,-1,-1]].
• cmd.ramp_update(name, range, color) → ramp_new(name, '', …) (creating.py:492-518).
• Volume ramps are separate: packages/engine/modules/pymol/colorramping.py:17-54 namedramps presets 2fofc, fofc, esp, rainbow, rainbow2 (built with the peak() helper, colorramping.py:14-15); volume_ramp_new(name, ramp) registers more (colorramping.py:56-84); volume_color(name, ramp, state) sets/gets (colorramping.py:123-181, C: _cmd.set_volume_ramp / _cmd.get_volume_ramp); ramp_expand flattens (v, colorname, a) or (v, r, g, b, a) into flat float lists (colorramping.py:265-298); ramp_to_colors interpolates to N colors (colorramping.py:231-263, note: it uses range(len(ramp) / 5) — Python-2 division, this function is broken on Python 3).
• volume_panel(name) opens the Qt volume ramp editor pmg_qt/volume.py (colorramping.py:183-227), which itself hosts a QColorDialog (pmg_qt/volume.py:414).

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C6. Chain / element / secondary-structure coloring

• _color_cycle (util.py:27-70) — 40 color indices, identical to C AutoColor (packages/engine/layer1/Color.cpp:35-76).
• cbc(selection, first_color=7, quiet, legacy=0) — “color by chain”, iterates cmd.get_chains, quotes chains containing spaces, uses _color_cycle[c % 40] unless legacy=1 (then first_color + c) (util.py:771-785). Aliased color_chains = cbc (util.py:819).
• color_objs(selection) — one color per object; when a real selection is given it also calls set_object_color (util.py:787-799).
• chainbow(selection, palette='rainbow') — per model, per chain, spectrum('count', palette, …, byres=1) (util.py:809-817).
• cbss(selection, helix_color='red', sheet_color='yellow', loop_color='green') — three cmd.color calls on ss H, ss S, not ss S+H (util.py:432-440).
• Element/carbon family: color_carbon (427), cnc (512, color atomic on non-carbon), cba(color, sel) (518, atomic on non-C + color on C + flags=1 object color), cbh(color, sel) (526, same but hydrogens), and the fixed-carbon shortcuts cbag (green, 442), cbac (cyan, 449), cbam (lightmagenta, 456), cbay (yellow, 463), cbas (salmon, 470), cbaw (white/hydrogen, 477), cbab (slate, 484), cbao (brightorange, 491), cbap (purple, 498), cbak (pink, 505).
• color_by_area(sele, mode='molecular', state=0, palette='rainbow') (util.py:80-119).
• util.colors('jmol') (util.py:1029-1040) — redefines hydrogen carbon nitrogen oxygen fluorine sulfur to Jmol values, sets auto_color 0, then color carbon, elem C + recolor.
• Deprecated: util.rainbow (993, prints deprecation, builds a 11-stop hex list), util.ss (1019), util.color_deep (801, forwards to cmd.color_deep).

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C7. The internal-GUI “C” (color) menu — packages/engine/modules/pymol/menu.py

• mol_color(sele) (menu.py:672-686) — root: by element, by chain, by ss, by rep, spectrum, separator, auto, separator, then the full color palette from all_colors.
• by_elem (menu.py:400-418) + by_elem2..by_elem6 (335-399) — 8 carbon-color choices per page, 6 pages; page 6 colors hydrogens via util.cbh. First entry is util.cnc (color non-carbon only).
• by_chain (menu.py:464-481) — util.color_chains over elem C / */CA / all; util.chainbow; spectrum('segi','rainbow', …) for elem C and all.
• by_ss (menu.py:420-426) — three util.cbss presets: red/yellow/green, cyan/magenta/salmon, cyan/red/magenta.
• by_rep / by_rep_sub (menu.py:428-444) — writes the per-rep color settings rather than atom colors, driven by rep_setting_lists (menu.py:482-517):
  • molecule: line_color, stick_color, ribbon_color, cartoon_color, label_color, dot_color, sphere_color, mesh_color, surface_color
  • measurement: dash_color, angle_color, dihedral_color, label_color
  • extra: cartoon_highlight_color, cartoon_ladder_color, cartoon_nucleic_acid_color, cartoon_ring_color, ellipsoid_color, label_outline_color, ray_interior_color, ray_trace_color, stick_ball_color Each submenu ends with an unset entry (cmd.unset(setting, sele)).
• spectrum (menu.py:446-462) — rainbow over elem C, */CA, byres; b-factors (all and */CA); util.color_by_area molecular/solvent.
• color_auto (menu.py:659-670) — color auto on elem C / all; util.color_objs on elem C / all.
• all_colors_list (menu.py:519-618) — the curated swatch palette, 9 groups: reds (11), greens (10), blues (9), yellows (7), magentas (10), cyans (7), oranges (7), tints (8), grays (11) — each entry a (3-digit swatch, color name) pair.
• all_colors_generic(expr) (menu.py:625-636) renders those groups and appends a ramps submenu built from colorramps (menu.py:620-623), which lists live object:ramp names cached by the menucontext singleton (menu.py:24-46).
• all_colors(sele) (menu.py:638-641) binds the expression to cmd.color_deep("{0}", <sele>, 0).
• vol_color (menu.py:643-653) — “panel” entry + one item per name in colorramping.namedramps.
• slice_color (menu.py:655-657), mesh_color (menu.py:696-709, adds negative-color submenu driving <rep>_negative_visible / <rep>_negative_color), measurement_color (687-694), general_color (711-712).

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C8. Color editor dialogs

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C9. Color LUT / color space

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PART D — REACT / BRIDGE MODEL

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D1. One introspection RPC drives both UIs

# bridge-side, built once at startup
def settings_catalogue():
    out = []
    for name, index in cmd.setting.index_dict.items():       # setting.py:39
        if name == 'ray_shadows':                            # setting.py:48 legacy alias
            continue
        t = cmd._cmd.get_setting_type(index)                 # Cmd.cpp:4394
        level = cmd._cmd.get_setting_level(index)            # Cmd.cpp:4403  (str)
        out.append({'name': name, 'index': index, 'type': t, 'level': level})
    return out

type SettingType = 0|1|2|3|4|5|6;      // blank|bool|int|float|float3|color|string
type SettingLevel = 'global'|'object'|'object-state'|'atom'|'atom-state'|'bond'|'bond-state';
interface SettingMeta {
  name: string; index: number; type: SettingType; level: SettingLevel;
  default?: number|number[]|string; min?: number; max?: number; help?: string;
}

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D2. Value RPCs

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D3. Change propagation

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D4. Component inventory

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D5. Client-side color evaluation

• specials −1..−7 must be resolved by the backend, not the client (ColorGetSpecial, Color.cpp:1789; front/back depend on bg_rgb, Color.cpp:1754-1788);
• 0x40RRGGBB-encoded colors decode client-side (Color.cpp:1847, viewing.py:2053);
• ramp colors (index <= -10) are position-dependent (ColorGetRamped, Color.cpp:189) and must be baked into vertex colors server-side;
• space rewrites the whole table through the LUT (Color.cpp:1680) — full re-fetch required.

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Constraints this area lives under

1. cmd.get_setting_updates() clears the changed flags as it reads (packages/engine/layer1/Setting.cpp:1128-1132). Two pollers = lost updates. The bridge must be the only caller, and any surviving Qt window must be disabled.
2. Defaults, min/max and help text are not exposed to Python anywhere (SettingInfo is static in Setting.cpp; packages/engine/data/setting_help.csv has zero consumers). Without a new accessor or a build-time extraction, the advanced table cannot show “default” or validate ranges.
3. get_setting_level exists in C (packages/engine/layer4/Cmd.cpp:4403) but has no Python wrapper — must be called as cmd._cmd.get_setting_level(i), which is undocumented/private and could change.
4. Setting indices are session-file ABI (packages/engine/layer1/SettingInfo.h:5-6). Any cached client-side catalogue keyed by index is safe across versions only if new settings are appended, never renumbered.
5. Wrong-level writes are silently accepted with only a console warning (packages/engine/layer3/Executive.cpp:12279-12286). The web UI must gate by level client-side or users will see “it saved but nothing happened”.
6. Float min/max declared in the table are never enforced (Setting.cpp:1890 checks type == cSetting_int only). Client-side validation is the only guard.
7. Menu items hardcode color indices (134, 104, 4236, 74, 104…) computed from the generated color-table layout (_gui.py:456-461,632,741). If a user runs set_color on a generated name or space changes the LUT, those labels lie. The web UI should resolve label→index at render time.
8. set_color auto-detects the 0–1 vs 0–255 range by “any component > 1.0” (viewing.py:2205-2207). A legitimate [1, 0, 0] in 0–255 space becomes red-in-0–1. Web pickers must always send 0–1 floats.
9. There is no event when colors change. Anything that calls set_color, ramp_new, space, load or reinitialize desynchronizes the client palette.
10. colorramping.ramp_to_colors uses Python-2 integer division (colorramping.py:243) and will raise on Python 3 — do not port it, reimplement in TS.
11. Color name lookup falls back to case-insensitive prefix matching in C (packages/engine/layer1/Color.cpp:736-748), which the source itself questions (“TODO does this even make sense?”). Two different lookup policies exist (C prefix match vs Python Shortcut in internal.py:566); the web client should send exact names to avoid divergence.
12. advanced_settings_gui writes with cmd.set(index, text); a bad value raises inside PyMOL and the table keeps showing the new text. Any port must round-trip the value back from the backend.
13. SettingGenerateSideEffects can invalidate reps and force geometry rebuilds (packages/engine/layer1/Setting.cpp:1872+). Setting changes are not cosmetic — the three.js scene may need a fresh geometry payload after almost any set.
14. 179 settings are atom/atom-state/bond/bond-state/object-level and are invisible to the current advanced table, which only reads globals. Feature parity with the desktop C menu (menu.rep_setting_lists) requires per-object/per-selection scope.

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Decisions this map fed

• No C accessor for SettingInfo default/min/max. The header is parsed instead (packages/bridge/tenmol_bridge/panels/settings.py); see D1.
• packages/engine/data/setting_help.csv (875 rows, zero upstream consumers) is the tooltip source. Row count does not equal setting count, so entries are matched by name and a missing row yields no tooltip rather than a wrong one.
• Menu writes keep log=1, quiet=0 so the browser’s command log mirrors desktop PyMOL’s .pml log.
• Per-object and per-selection scope is offered wherever the level allows it (apps/web/src/features/settings/atomSettings.ts), because 179 settings are atom/atom-state/bond/bond-state/object level and the Qt advanced table only ever read globals (constraint 14).
• The generated bands (s000…, r, c, w, o) sit behind an “advanced” toggle, not in the default palette: apps/web/src/features/colors/SwatchGrid.tsx is pymol.menu.all_colors_list (80 tiles) and BandGrid.tsx pages through the remaining 5388 slots. They cannot be dropped — spectrum, ramp_new and the constants_palette palettes are expressed in those names.
• atomic/object/front/back are guarded on index < 0, not index == -1. They resolve to -4/-5/-6/-7 and cmd.get_color_tuple returns None for all of them (packages/engine/layer4/Cmd.cpp:1336); the Qt dialog tests only -1 (pymol_qt_gui.py:558) and raises TypeError on the others.