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Dialogs: volume, properties, scenes, shortcuts, settings, text editor

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0. How these dialogs are opened (entry points)

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1. Volume Color Map Editor (packages/engine/modules/pmg_qt/volume.py, 877 lines)

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1.1 Container

• VolumePanelDocked(parent, ...) — volume.py:811-821: builds a QDockWidget, added to Qt.DockWidgetArea.BottomDockWidgetArea of the main window. VolumePanel = VolumePanelDocked (volume.py:830) — this is what ships.
• VolumePanelDialog(parent, ...) — volume.py:824-827: plain modeless QDialog variant (unused by default).

1. VolumeEditorWidget canvas (stretches; sizeHint 600x200, volume.py:98-99)
2. Button row (volume.py:864-871):
   • QPushButton "Get colors as script" -> displayScript (volume.py:847-849)
   • QPushButton "Reset Data Range" -> editor.reset (volume.py:853-855)
   • QPushButton "Help" -> displayHelp (volume.py:850-852)
   • stretch
   • QCheckBox "Update volume colors in real-time" (objectName volume_checkbox), default checked, min width 30 (volume.py:856-862) -> toggleRealTimeUpdates (volume.py:423-424)
   • All push buttons set setAutoDefault(False).

histogram = cmd.get_volume_histogram(name)   # list len = bins+4 (default bins=64)
widget.editor.setHistogram(histogram)
colors    = cmd.volume_color(name)           # flat [v,r,g,b,a] * N
widget.editor.setColors(colors)

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1.2 Data contracts

• cmd.get_volume_histogram(objName, bins=64, range=None) (packages/engine/modules/pymol/querying.py:62-72) -> [min, max, mean, stdev, h0..h(bins-1)]; C entry CmdGetVolumeHistogram / ExecutiveGetHistogram (packages/engine/layer4/Cmd.cpp:738-752).
• cmd.volume_color(name, ramp='', state=CURRENT_STATE, quiet=1, _guiupdate=True) (packages/engine/modules/pymol/colorramping.py:123-181). With empty ramp it is a getter (delegates to get_volume_color, colorramping.py:87-121, C _cmd.get_volume_ramp), returning a flat list of 5-tuples v, r, g, b, a (floats, RGB in 0..1). With a ramp it is a setter (_cmd.set_volume_ramp, colorramping.py:156).
• Named presets namedramps (colorramping.py:17-54): 2fofc, fofc, esp, rainbow, rainbow2; extendable via cmd.volume_ramp_new(name, ramp) (colorramping.py:56-84). These are exposed in the internal A > volume menu (packages/engine/modules/pymol/menu.py:644-654).
• Ramp string parsing: ramp_expand (colorramping.py:265-298) accepts v color a ... or v r g b a ..., raises ValueError("malformed color ramp").

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1.3 The canvas widget — exact interaction model

1. paintGrid — axis lines + 9 dashed horizontal grid lines (volume.py:101-117)
2. paintAxes — integer ticks on x (only drawn if labels do not collide: if x - lastx > w + 2*fw, volume.py:218-227), 0.1..0.9 ticks on y with the same anti-collision rule (volume.py:232-239), plus three editable value boxes (volume.py:242-249)
3. paintHistogram (clipped to plot rect) — a red polyline resampled per pixel column with linear interpolation, remapped for the current zoom window (volume.py:148-177)
4. paintColorDots — polyline connecting all points in gray, then a filled circle per point using its RGB; the hovered point is drawn again with radius DOT_RADIUS + 2 (volume.py:119-146)
5. paintZoomArea — translucent rgba(0,64,128,128) rectangle between init_pos.x() and zoom_pos.x() while ctrl+right-dragging (volume.py:251-255)

• Left-click a box -> QInputDialog.getDouble (enterValue, volume.py:281-290, decimals=6) with these validation ranges (volume.py:294-309):
  • amax: title “Maximum Alpha Value”, range [EPS, 1.0]
  • vmin: title “Minimum Data Value”, range [-1e8, vmax - EPS]
  • vmax: title “Maximum Data Value”, range [vmin + EPS, 1e8] Cancel keeps the old value (enterValue returns value if not accepted).
• Mouse wheel over a box (wheelEvent, volume.py:533-545), delta = -angleDelta.y()/1000:
  • amax -> clamp(amax*(1+delta), 0, 1)
  • vmin -> min(vmin + (vmax-vmin)*delta, vmax - EPS)
  • vmax -> max(vmax + (vmax-vmin)*delta, vmin + EPS) Box wheel does not push colors to PyMOL (early return at volume.py:545).
• Mouse wheel not over a box (volume.py:547-554) scales every point’s alpha: y -= y*delta, clamped to [0,1], then repaint + updateVolumeColors() unconditionally (ignores the real-time checkbox).

• L-Click -> add 1 point at cursor, color from the 6-color cycle (addPoint, volume.py:607-634); sets dragged = True so the release does not open the color picker (volume.py:322).
• Ctrl + L-Click -> add 3 points (isosurface preset): the clicked point plus two zero-alpha points at ±10 px (volume.py:625-630).
• Ctrl + R-Drag -> zoom band; on release vmin, vmax = sorted([xToData(convertX(x0)), xToData(convertX(x1))]) (volume.py:356-362). Zero-width drag is ignored.

• L-Click (release, not dragged) -> open QColorDialog for that point (setPointColor, volume.py:406-421). The dialog is modal (.open()), reused across invocations, with currentColorChanged wired to updatePointColor (live preview, volume.py:387-393) and finished wired to colorDialogClosed (volume.py:395-404) which restores self.original_color on Reject.
• Ctrl + L-Click -> same color dialog but applies to the point and its two neighbours (changePointColor with color_triple, volume.py:367-385).
• R-Click (no modifier, or Ctrl — see the comment at volume.py:329) -> edit the data value via enterValue("Data value", ...) clamped to [prev_point.x or vmin, next_point.x or vmax] (volume.py:330-335).
• Shift + R-Click -> edit the alpha/opacity via enterValue("Alpha value (opacity)", value, 0.0, 1.0) (volume.py:336-339).
• M-Click (middle) or Shift + L-Click -> remove the point (volume.py:344-348, removePoints, volume.py:636-649).
• Ctrl + M-Click or Ctrl + Shift + L-Click -> remove 3 points (removePoints(three_points=True)).
• L-Drag -> move the point in both axes (movePoints, volume.py:556-605); x is clamped so points cannot cross their neighbours (volume.py:568-583). A QToolTip follows the cursor showing "value: %.3f\nalpha: %.3f" (volume.py:602-603).
• Ctrl + L-Drag -> move 3 points, horizontal only (delta = 2 selects neighbour-of-neighbour bounds, and new_y = y when delta > 1, volume.py:561, volume.py:588, volume.py:592-599).
• R-Drag -> axis-constrained move: the axis is latched on the first move from abs(dx) > abs(dy) ? 'x' : 'y' (volume.py:502-507), applied at volume.py:587-588.
• Hover (no buttons) -> hover_point tracked and repainted with a larger dot (volume.py:509-517, setMouseTracking(True) at volume.py:73).
• Hit region for press/hover is the plot rect inflated by DOT_RADIUS on all sides (volume.py:311-313, volume.py:510-511).

self.ignore_set_colors = True
self.cmd.volume_color(self.volume_name, self.getColors())
self.ignore_set_colors = False

• reset() (volume.py:739-746) — restores vmin/vmax to original_vmin/original_vmax and re-pushes colors. It does not touch the points.
• displayScript() (volume.py:775-799) — builds a cmd.volume_ramp_new('ramp%03d', [...]) snippet with a random 3-digit name and shows it in a reusable read-only monospace QPlainTextEdit dialog (displayTextDialog, volume.py:748-767, width 500). Identical text is also printed by get_volume_color(..., quiet=0) (colorramping.py:106-114).
• displayHelp() (volume.py:769-773) — shows the VOLUME_HELP block verbatim (volume.py:30-66).
• setColors(colors) (volume.py:711-737) — external ingestion, 5 floats per point, aborts with a warning if any value is NaN.
• windowTopLevelChanged(floating) (volume.py:801-808) — dead code; the connection is commented out at volume.py:818-819 and is_floating is hardcoded True at volume.py:267.

• __init__ sets self.constrain = None (volume.py:89) but the drag code reads and writes self.constraint (volume.py:318, volume.py:503, volume.py:587-588). self.constrain is dead.
• movePoints uses the Qt5-only event.x() / event.y() (volume.py:565, volume.py:584) while wheelEvent already uses the Qt6 form event.position().toPoint() (volume.py:534). Mixed API generation.
• paintHistogram computes y against rect.height()-2 rather than rect.top() (volume.py:155, volume.py:168), so the curve is anchored to the widget, not to the plot rect.

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2. Properties Inspector (packages/engine/modules/pmg_qt/properties_dialog.py, 415 lines + forms/props.ui)

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2.1 Form props.ui (QWidget "Form", windowTitle “Properties Inspector”, 400x500)

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2.2 Tree structure (built in setup_tree_widget, properties_dialog.py:69-117)

Object-Level                       (cat)
  TTT Matrix                       (entry, editable)
  Settings                         (cat, dynamic)
Object-State-Level                 (cat)
  Title                            (entry)
  State Matrix                     (entry)
  Settings                         (cat, dynamic)
  [Properties]                     (Incentive-only; = Ellipsis in open source, line 80)
Atom-Level                         (cat)
  Identifiers                      (cat)
  Properties (built-in)            (cat)
  Settings                         (cat, dynamic)
  [Properties]                     (Incentive-only; = Ellipsis, line 86)
Atom-State-Level                   (cat)
  Properties (built-in)            (cat)
  Settings                         (cat, dynamic)

• keys_atom_identifiers (properties_dialog.py:92-95): model, index, segi, chain, resi, resn, oneletter, name, alt, ID, rank
• keys_atom_builtins (properties_dialog.py:96-103): elem, q, b, type, formal_charge, partial_charge, numeric_type, text_type, vdw, ss, color, reps, flags, label, cartoon, protons, geom, valence, elec_radius — note stereo is deliberately commented out to avoid stereo auto-assignment errors (properties_dialog.py:98-99).
• keys_astate_builtins (properties_dialog.py:104): state, x, y, z

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2.3 Data sources (getters)

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2.4 Effects (setters), triggered from item_changed (properties_dialog.py:150-227)

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3. Scene Panel (packages/engine/modules/pmg_qt/scene_bin_gui.py, 397 lines)

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3.1 Widgets

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3.2 Data source

• cmd.get_scene_list() -> _cmd.get_scene_order() (scene_bin_gui.py:244-251; API packages/engine/modules/pymol/viewing.py:919-921).
• cmd.get_scene_thumbnail(name) -> raw PNG bytes loaded into a QPixmap (scene_bin_gui.py:183-192; API viewing.py:923-925; C packages/engine/layer4/Cmd.cpp:1159-1173, backed by MovieSceneGetThumbnail, packages/engine/layer3/MovieScene.cpp:45).
• Message and actions columns are hardcoded placeholders 'This is a base message' / 'Rock, zoom, something' (scene_bin_gui.py:170-171). The real APIs exist and are unused here: cmd.get_scene_message(name) / cmd.set_scene_message(name, message) (packages/engine/modules/pymol/viewing.py:927-933).

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3.3 Effects

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3.4 Validation & refresh model

• Rename validation (_rename_scene, scene_bin_gui.py:360-377): rejects names containing a space (“Scene names with spaces are not supported”) and blank names (“Blank scene names are not allowed”) — both only print() to the console and revert the table. No modal error.
• Reorder detection is heuristic: _check_table_state (scene_bin_gui.py:339-349) diffs the model order against cmd.get_scene_list(), and only calls _reorder_scenes if more than one position differs — that is how it disambiguates “drag” from “rename”.
• _compare_scene_lists (scene_bin_gui.py:309-318) compares positionally over min(len) and returns [old, new] pairs.
• _get_table_scene_list (scene_bin_gui.py:320-337) derives order from rowViewportPosition(row)/100 (hardcoded to the 100 px row height) and sorts by it.
• eventFilter (scene_bin_gui.py:102-113) is installed on the table viewport and reacts to raw numeric event types: 12 (paint) -> _check_table_state() on every repaint, 24 (window-activate) -> full _populate_data(). This is a polling design and is the main thing to replace with a proper event subscription on the web side.
• _selection_changed (scene_bin_gui.py:351-358) enables/disables the Delete and Update buttons.
• _update_scene_dict (scene_bin_gui.py:154-181) builds/prunes the cache and, note, appends a 4th element (scene_position) to a list whose enum only defines three indices (scene_bin_gui.py:172-174).

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4. Keyboard Shortcut Menu (packages/engine/modules/pmg_qt/shortcut_menu_gui.py, 415 lines)

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4.1 Widgets

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4.2 Sub-dialogs loaded via load_form (shortcut_menu_gui.py:62-64)

• keyLabel “Key:”, keyEdit (QLineEdit, readOnly, placeholder “Press Key”)
• commandLabel “Command:”, commandEdit (QLineEdit, placeholder “Type Command”)
• helpButton “Help” (setDefault(False), setAutoDefault(False), shortcut_menu_gui.py:282-283) -> shows help_shortcut
• createButton “Create Shortcut” -> create_new_shortcut_caller

• keyevent_to_string (:301-315) — joins modifier names from _SHORTCUT_MODIFIER_MAP (:25-30) with the key name from _SHORTCUT_KEY_MAP (a reverse map of every Qt.Key enum member, built at :15-23).
• process_keyevent_string (:317-344) — normalizes to PyMOL prefixes: Control/Meta -> CTRL, Control+Shift -> CTSH, Alt -> ALT, Shift -> SHFT; and remaps special names through _REPLACE_KEYS (:32-42: PageUp->pgup, PageDown->pgdn, Home->home, Insert->insert, Up->up, Down->down, Left->left, Right->right, End->end). Result is joined with - (e.g. CTRL-F5).
• Keys in ShortcutManager.reserved_keys are swallowed and never displayed (shortcut_menu_gui.py:293-294); reserved set is ('CTRL-S','CTRL-E','CTRL-O','CTRL-M','up','down') (packages/engine/modules/pymol/shortcut_manager.py:21).

• label “Are you sure you want to change this existing key binding?” (centered)
• doNotShowCheckBox “Don’t show this again”
• cancelButton “Cancel” -> hide (shortcut_menu_gui.py:355-356)
• confirmButton “Confirm” -> create_new_shortcut(confirm_new_key, confirm_new_binding)
  • populateData() + hide (shortcut_menu_gui.py:350-354)

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4.3 Backing model (packages/engine/modules/pymol/shortcut_manager.py, packages/engine/modules/pymol/shortcut_dict.py)

• ShortcutIndex enum: COMMAND=0, DESCRIPT=1, USER_DEF=2 (shortcut_manager.py:8-11).
• cmd.shortcut_dict is a deep-ish copy of shortcut_dict_ref (shortcut_manager.py:18), the canonical default table in packages/engine/modules/pymol/shortcut_dict.py:11-136 — 135 default bindings, covering left/right/pgup/pgdn/home/end/insert, their SHFT-/CTRL-/ALT-/CTSH- variants, CTRL-A/C/F/H/I/L/T/V/X/Y/Z, ALT-0..9, ALT-A..Z (fragment and amino-acid attach commands), CTSH-A..Z (editing/replace commands), and CTRL-F1..F12 / CTSH-F1..F12 (scene store).
• get_default_keys (packages/engine/modules/pymol/keyboard.py:87-93) projects shortcut_dict_ref to {key: default_command}.
• check_saved_dict (shortcut_manager.py:23-31) merges the user file into the table; check_key_mappings (:33-68) reconciles three sources — cmd.key_mappings (live), default_bindings, cmd.shortcut_dict — marking mismatches as user-defined, empty mappings as 'Deleted', and creating rows for keys bound with cmd.set_key outside the GUI.
• Persistence: save_shortcuts (shortcut_manager.py:70-76) prunes unused keys (remove_unused, :78-88) then JSON-dumps to ~/.pymol/shortcuts_save.json (packages/engine/modules/pymol/save_shortcut.py:6, 18-36). Load on startup: load_and_set (save_shortcut.py:65-71) called from pymol_qt_gui.py:419 and passed into the dialog at pymol_qt_gui.py:888.
• reset_all_default (shortcut_manager.py:90-116) re-set_keys everything, supports both string and (fn, args, kwargs) tuple bindings, deletes keys with no default from both shortcut_dict and cmd.key_mappings, prints “Restored default keybindings”.
• create_new_shortcut (shortcut_manager.py:118-139) wraps cmd.set_key in try/except printing “This cannot be bound.” / “This key is reserved.”.

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4.4 Row-level actions

• Edit command cell (itemChanged, shortcut_menu_gui.py:393-415): cmd.set_key(key, text) + write shortcut_dict[key][2]; description column is set to 'user defined' only when no filter is active (:408-411) — a known wart, because the proxy model row index differs from the source row index. Rows whose text is "Deleted" are skipped (:401).
• Delete Selected (:219-245): cmd.set_key(key, ''); keys that have a default become the literal string "Deleted" in both value columns, keys without a default are removed from the model and from shortcut_dict, with a console message "<key> has been deleted and will be removed from the table". Note it iterates over selectedIndexes(), i.e. once per selected cell.
• Reset Selected (:247-274): restores the default command/description and re-set_keys; prints “This key does not have a default value.” otherwise.
• Reset All (:211-217), Save (:145), Refresh (:204-209, re-runs check_key_mappings then populateData).
• intial_populate (:195-202) runs check_saved_dict + check_key_mappings once at open.
• After each populateData the selection model is re-connected (shortcut_menu_gui.py:188) — repeated connects accumulate.

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4.5 cmd.set_key contract

• key.rpartition('-') -> modifier must be in internal.modifier_keys = ['', 'SHFT', 'CTRL', 'CTSH', 'ALT'] (packages/engine/modules/pymol/internal.py:390-396), else CmdException("not a valid modifier key: '<mod>'.").
• Multi-char patterns not starting with F are lowercased and must be in internal.special_key_names (derived from special_key_codes, internal.py:398-425: F1..F12, left, up, right, down, pgup, pgdn, home, end, insert), else CmdException("special '<pat>' key not found.").
• Single character with no modifier -> CmdException("Can't map regular letters."); with SHFT -> CmdException("Can't map regular letters with SHFT.").
• Stores into cmd.key_mappings[key], value is either a command string or a (fn, args, kwargs) tuple. Dispatch at runtime: internal._invoke_key (internal.py:426-445) and internal._special (internal.py:447-...).
• Qt->PyMOL key translation for the viewport lives in packages/engine/modules/pmg_qt/keymapping.py:10-97 (keyMap, specialMap, keyPressEventToPyMOLButtonArgs, modifier mask 0x1 Shift / 0x2 Ctrl-or-Meta / 0x4 Alt) — the web client needs the same mapping to forward viewport keys.

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5. Advanced Settings (packages/engine/modules/pmg_qt/advanced_settings_gui.py, 99 lines)

• filter_le (QLineEdit, placeholder “Filter”) -> proxy_model.setFilterRegularExpression (:25-28)
• table (QTableView) over QSortFilterProxyModel/QStandardItemModel (:18-20, :32-34); both headers hidden, columns auto-sized (formatTable, :69-80)

• checkable -> cmd.set(index, checked, log=1, quiet=0)
• otherwise -> cmd.set(index, item.text(), log=1, quiet=0) log=1 means the change is echoed into the PyMOL log file; quiet=0 prints to the feedback browser. No validation, no error handling — a bad value raises inside cmd.set and only prints. No refresh — the table never re-reads values after opening, so settings changed from the command line go stale.

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6. Text Editor (packages/engine/modules/pmg_qt/TextEditor.py, 195 lines)

• File: Open (Ctrl+O) -> doOpen; Save (Ctrl+S) -> doSave; Save as ... (Ctrl+Shift+S) -> doSaveAs
• Syntax: exclusive QActionGroup of checkable actions Python / PML / Plain Text (keys python, pml, plain) -> setSyntax(key)

• _open(filename) (:28-46): reads the file if it exists, otherwise starts empty; auto-selects syntax by extension — .py -> python, .pml or a name ending in pymolrc -> pml, else plain.
• setSyntax(filetype='plain') (:48-60): checks the menu action, detaches the old highlighter, imports pmg_qt.syntax.<filetype> and instantiates Highlighter(self.text.document()). Available modules: packages/engine/modules/pmg_qt/syntax/python.py (147 lines), packages/engine/modules/pmg_qt/syntax/pml.py (119 lines, class Highlighter at syntax/pml.py:30, uses syntax/pmlparser.py:parse_pml). There is no syntax/plain.py, so setSyntax('plain') hits the ImportError branch and simply leaves the document unhighlighted (TextEditor.py:57-58).
• doSaveAs (:69-77): QFileDialog.getSaveFileName starting in the current file’s directory; writes and re-points self.filename.
• doSave (:79-83): falls back to Save-As when there is no filename.
• doOpen (:85-91): check_ask_save() gate, then QFileDialog.getOpenFileNames, opens fnames[0] only.
• check_ask_save (:93-103): if the buffer differs from _savedcontent, a modal QMessageBox.question “Save?” / “Save changes?” with Yes / No / Cancel (default Yes); Cancel aborts the operation.
• closeEvent (:105-109): same gate; event.ignore() on Cancel.

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7. Full packages/engine/modules/pmg_qt/forms/ inventory

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7.1 Widget lists (as declared in the XML)

• askpartial.ui: label (“The current PyMOL window has a session in progress. How do you want to proceed?”), check_discard (QRadioButton “&Discard current session”, checked), label_3, check_partial (QRadioButton “&Merge with current session (partial load)”, tip partial=1), label_2, check_rename (QCheckBox “Automatically rename duplicate objects”, tip auto_rename_duplicate_objects (global setting)), check_new (QRadioButton “Open &in new PyMOL Window”), label_4, buttonBox (QDialogButtonBox).
• change_confirm.ui: label, doNotShowCheckBox, confirmButton, cancelButton (see §4.2).
• colors.ui: list_colors (QListWidget), frame_color (QFrame swatch), input_name (QLineEdit) + label_4 “Name”, input_R/G/B (QDoubleSpinBox max 1.0 step 0.01) + label/label_2/label_3 “Red”/“Green”/“Blue”, slider_R/G/B (QSlider max 100), button_apply (“Apply”).
• create_shortcut.ui: keyLabel, keyEdit (readOnly, “Press Key”), commandLabel, commandEdit (“Type Command”), helpButton, createButton.
• fetch.ui: label (fetch_path hyperlink note), label_2 “PDB ID:”, input_code (QLineEdit, “4 letter PDB code”), input_check_pdb (checked), input_check_2fofc, input_check_fofc, input_name, input_name_2fofc, input_name_fofc (all “Object name (optional)”), groupBox “PDB Structure Options”, label_3 “Chain name (optional):”, input_chain (editable QComboBox), label_4 “Assembly (optional):”, input_assembly (editable QComboBox), groupBox_2 “This will run the following command”, output_command (QLabel “fetch …”), button_ok (“Download”).
• help_shortcut.ui: label, line, textBrowser.
• load_aln.ui: label_column_input (“PyMOL Object”), button_cancel (“Cancel”), button_ok (“Load”). Note: the object-column widgets are generated at runtime in file_dialogs.py, not in the XML.
• load_mae.ui: input_mimic (checked, “Use settings to match cartoon/ribbon color and ballstick style”), label_3 “Object/group name” + input_object_name, label “Object properties” + input_object_props (default *), label_2 “Atom properties” + input_atom_props (default *), label “Multiple entries” + input_multiplex (QComboBox: “automatic handling”, “as one multi-state object (trajectory)”, “as one multi-state object (discrete states)”, “as separate objects”), groupBox_2 + output_command, button_ok (“Load”).
• load_map.ui: groupBox_3 “Map Object” [input_object_name, input_normalize (checked), label normalization caveat], groupBox “Representation” [label_2 “se&lection” + input_selection (editable combo: (blank), enabled, sele, center), label_3 “b&uffer” + input_buffer (default 2.0), check_carve, label_4 “level” + input_level (min -99, default 1.0, 4 decimals, step 0.1), check_volume + input_name_volume, check_isosurface + input_name_isosurface, check_isomesh + input_name_isomesh], groupBox_2 + output_command, button_ok.
• load_mtz.ui: groupBox “Column Labels” [label_4 “Amplitudes” + input_amplitudes, label_5 “Phases” + input_phases, label_6 “Weights” + input_weights — all QComboBox], groupBox_2 “Resolution” [label “Low” + input_reso_min (50.0), label_2 “High” + input_reso_max (1.0)], groupBox_3 “Map Options” [label_3 “New Map Name Prefix” + input_prefix], buttonBox.
• load_traj.ui: groupBox “Target Object” [label + input_object (combo), label_3 “State” + input_state (max 999, default 1, tip “Append if state=0”)], groupBox_3 “Frames” [input_start (1..99999, 1), input_stop (-1..99999, -1, tip “Load entire trajectory if stop < 1”), input_interval (min 1)], groupBox_4 “Memory Optimization” [input_dbm3 “defer_builds_mode=3 (don’t keep geometry for other states in memory)”], groupBox_2 + output_command, button_ok.
• movieexport.ui: group_format “Movie Format” [label “E&ncoder” + input_encoder (blank, ffmpeg, mpeg_encode, convert), label_quality + input_quality (60..100, default 90, suffix %), radios format_mp4, format_mpg, format_mov, format_gif, format_png (checked)], label_2 “Wid&th” + input_width (max 9999), label_3 “Hei&ght” + input_height, label_7 “Common:” + button_720p/button_480p/button_360p, group_mode “Rendering” [input_draw (checked), input_ray], button_ok (QCommandLinkButton “Save Movie as …”).
• pluginitem.ui: w_title, w_version, w_loadtime, w_info (“Info”), w_enable (“Load”), w_startup (“Load on startup”), w_settings (“Settings”), w_uninstall (“Uninstall”).
• pluginmanager.ui: tabWidget with 4 tabs — tab1 (e_filter, c_loaded, c_startup, f_installed_scroll/f_installed_widget, b_startup_all, b_startup_none), tab2 (groupBox “Install from local file” + b_local; groupBox_2 “Install from PyMOLWiki or any URL” + label, label_2 “URL:”, e_wiki, b_wiki “Fetch”; groupBox_3 “Install from Repository” + l_repositories, b_add_repo, b_remove_repo, l_repo_plugins, b_info, b_install), tab3 (groupBox_4 “Plugin override search path” + slb_path, bb_path_add, bb_path_remove, bb_path_up, bb_path_down, label_4 restart notice; groupBox_5 “Preferences” + t_preferences), tab4 (textBrowser).
• png.ui: label (2.0 note), input_rendering (QComboBox: “capture current display”, “draw antialiased OpenGL image”, “ray trace with opaque background”, “ray trace with transparent background”), button_ok (QCommandLinkButton “Save PNG image as …”).
• props.ui: see §2.1.
• render.ui: stack (QStackedWidget, 2 pages). page_1: label “Width” + input_width (px, max 99999) + input_width_units (suffix cm, max 999), label_2 “Height” + input_height/input_height_units, button_current (“Reset”, tip “Use current viewport size”), button_lock (“Lock aspect ratio”, checked), label_5 “Units” + input_units (cm/inch), label_3 “at” + input_dpi (editable combo 300/150/90, currentIndex 1) + label_4 “DPI”, input_transparent (“transparent background (“Ray” only)”, checked), line_2, button_draw (“Draw (fast)”), label_6 ”- or -”, button_ray (“Ray (slow)”). page_2: button_save (“Save Image to File”), button_clip (“Copy Image to Clipboard”), button_back (”< Back”).
• save_molecule.ui: label_2 “Se&lection” + input_selection (editable combo: enabled, all), label “S&tate” + input_state (“-1 (current)”, “0 (all states)”), tabWidget with 3 tabs — tab_3 (input_retain_order), tab_4 (input_no_pdb_conect_nodup, input_pdb_conect_all, input_no_ignore_pdb_segi, input_pdb_retain_ids, input_multisave), tab (label_3 “Write objects or states to …”, input_multi_off (checked), input_multi_object + input_multi_object_fmt ({name}), input_multi_state + input_multi_state_fmt ({name}_{state}), input_multi_prompt (checked)), button_ok (“Save…”).
• save_object.ui: label “Object”, input_name (QComboBox), button_ok (“Save…”).
• shortcut_menu.ui: shortcutTable, showAllButton, showBasicButton, addNewButton — dead.

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8. Bridge / API surface for this area

1. volume ramp changed externally -> colorramping.py:170-179 calls panel.widget().editor.setColors(ramplist). In the port the ramp is re-read per object (packages/bridge/tenmol_bridge/panels/volume.py, apps/web/src/features/volume/ramp.ts).
2. scene list / order / thumbnails changed -> Qt discovers this by paint-time and window-activate polling (scene_bin_gui.py:102-113); the port carries it on the scenes topic (packages/protocol/src/topics/scenes.ts).
3. settings changed from the command line -> Advanced Settings has no refresh at all in Qt; pymol_qt_gui.py:110-115 shows the setting_callbacks mechanism (index -> callable) that the settings topic generalises (see docs/settings-colors.md D3).
4. picked atom (pk1) changed -> the Properties Inspector only reads pk1 on open and on Refresh (properties_dialog.py:324-328, 406-415); the port re-reads it from the selection topic (apps/web/src/features/properties/service.ts).