Choose the actor
Use the viewport selection or another component from the cast. A generated unit and independent molecular rig can move on their own.
Build a cast from any structures, click a molecule in the frame, and direct it with the same gestures used to arrange a shot. Drag to place it, draw its route, turn on Auto-key to record poses, or drop it onto another component to create an editable dock or bind relationship. Right-click, or long-press on touch, puts the most-used object, animation, contact, procedural assembly, representation, visibility and scene commands under the pointer.
No-code · Ordinary records
Build motion from anything
Turn any saved molecular selection into a component, then stack general behaviours and relationships. Every layer remains independent and editable.
Directly in the viewport
Click or tap a component, choose a tool, then drag. Auto-key writes one readable Pose lane; Path turns the gesture into a smooth editable route. Right-click or long-press opens contextual transforms, animation, contacts, procedural generation, style, visibility and object actions.
Interaction
Ligand → Protein · bind & follow
Approach 2.0 s · dock · release 4.0 s · response linked
Start here · one action at a time
Press Director in the studio top bar. Create, Animate, Connect, Build, Sculpt, Shots and Finish follow the order of making a film, while the Guided animation turns plain-language choices into unrestricted ordinary records.
Use the viewport selection or another component from the cast. A generated unit and independent molecular rig can move on their own.
Move somewhere, Approach / meet, Bind / follow, Rotate / flex, Grow / assemble or choose any Custom behaviour.
Draw the route in the frame, choose Straight movement, pick a target component, choose a flex, or set an assembly origin.
Use the playhead, the actor’s last action, the shot opening or midpoint, or exact Start and Duration with Quick, Natural or Deliberate pacing.
Choose No added response, Brief highlight, Soft physical contact, or Pause, then release. Ripple Å and Ripple time stay editable.
Create step or Create + play writes normal keys, clips, ports, constraints, relationships and generators plus transparent Motion Block metadata.
Choose Start drawing in viewport, drag the component through the desired route, then return to the guide and press Next. The sampled Pose keys are retimed into the interval you chose. For a direct move, choose Straight movement, press Place destination ghost, and click the end point before choosing timing. For direct work, use Navigate, Pick, Move, Path, Rotate, Depth, Scale and Auto-key. Auto-key off adjusts setup; Auto-key on writes a grouped Pose key at the playhead.
Focus viewport maximises the live frame in Animate. Restore workspace or Esc returns the cast, guide and timeline. Cast and Timeline become drawers on narrow screens.
Click or tap to pick, then drag with the active tool. Right-click opens the contextual menu; on touch, long-press without moving. From a keyboard use the Context Menu key or Shift F10, arrows, Home/End, Enter and Esc. ⌘ K / Ctrl K searches every Director command.
The menu’s Animate outcome section contains Move along a route…, Meet at chosen points…, Bind at chosen points…, Flex around this point… and Grow or assemble from here…. Object actions include Frame selection, Open guided animation, Change appearance…, Make the camera follow… and procedural assembly. Cartoon/Surface/Ball + stick/Spacefill, full Style, hide/isolate/lock, duplicate and safe removal remain under the pointer. Empty-space actions frame or reveal the scene, add a molecule, open Motion Lab or render a still. Large outcomes open their full Director workspace; small changes happen in place.
In Connect choose Moving and Target, then Approach, Dock, Bind & follow or Follow. It can infer the nearest visible atoms. For the fastest exact handoff, right-click the moving surface site and choose Meet at chosen points… or Bind at chosen points…; the first pin stays fixed while you click the exact target site on another component. Director then opens with both points retained.
Inside the guided step, Pick exact surface points also provides Pick moving pin, Pick target pin, Preview contact and Confirm points. The viewport keeps coloured pins, normals, a dock ghost, gap and clash feedback visible.
Tune Start, Approach time, Gap (Å), point/rigid/soft/hinge/slider Contact, Stay connected or Release after dwell, and Dwell.
This is authored spatial direction. It does not calculate a docking energy, affinity or preferred binding pose.
On a Molecular Surface, the pin uses the visible triangle, barycentric position and normal. On Cartoon or trace, the clicked ribbon stays as a dashed visual cue while contact resolves to that residue’s atom/probe envelope. Spacefill, Ball + stick and Sticks use the visible atom envelope. A Shape Lab object uses its visible mesh triangle.
Amber marks the moving point; cyan marks the target. Both stay actor-local as components move. A visible atom may be labelled as an atomic-site fallback; a missing molecular-surface or custom-mesh hit never invents a component-centre pin and instead asks you to repick.
Right-click the intended cue and choose Flex around this point…, or select Rotate / flex in Guided animation. Press Pick region endpoints, then click two points on the same component. The owned residue range, explicit pivot, hinge axis and bend arc remain visible before creation. Choose Flex and return, Rotate, Organic drift, Breathe or Step / ratchet, then open More control for Angle °, hold/return or step timing.
The child component and pivot are authored controls, not a predicted conformational pathway. The ordinary behaviour clip can be retimed, layered, disabled or deleted.
Right-click the intended origin and choose Grow or assemble from here…. In Grow / assemble, choose the Assembly origin and press Place path. Place the endpoint, adjust depth, and optionally add a bend; the measured target-local path genuinely drives the retained-unit placement. Set Units, Layout, Rise Å, Twist ° and Radius Å under More control. The result is an editable generator, not a one-off mesh or fixed preset.
Count, unit, path, spacing, orientation, timing, layout and responses stay available after creation. The construction rule does not infer polymer chemistry, sequence, stoichiometry, assembly order or feasibility.
Right-click Change appearance… for the full material and texture workspace. For a timed cue, choose Custom behaviour → Appearance / reveal, then Reveal, Conceal or Pulse highlight. Pick appearance cue marks the component and identifies the active representation that will change before the ordinary effect clip is created.
Appearance is editorial unless it is explicitly mapped to cited structural data. A reveal or highlight does not alter deposited coordinates.
Soft physical contact / Physical ripple on arrival creates a real Å-scale displacement wave on the receiving ribbon, surface, atoms and sticks. Tint, roughness and micro-normal travel on that same geometry; glow is optional. Amplitude and time are independent and the default is restrained.
Brief highlight, Contact Flash, Molecular Ripple, Energy Arc and Particle Burst are visual cues. They can clarify the story but do not move the surface. Both kinds are illustrative—not molecular dynamics—and leave deposited and trajectory coordinates unchanged.
For a visible response that is not the contact ripple, choose Custom behaviour → Component response, choose the motion, then press Pick response origin. The overlay shows the point and axis. Choose This component only or Through completed contacts; contact reach is previewed only for the latter and its ordinary clip retains hops, delay and falloff.
A reaction cue explains causality in the film; it is not evidence of an allosteric pathway, kinetics or force propagation unless backed by imported simulation data.
Right-click a component and choose Make the camera follow…, or choose Custom behaviour → Camera move. Select Compose a camera move, choose the Camera focus target, then press Compose destination view. The handoff keeps its exact camera mode, framing and focus metadata beside the ordinary start and destination camera tracks.
This is separate from Focus viewport, which only changes the authoring layout. Camera movement, tracking and depth of field are editorial and make no molecular claim.
Choose Orbit when you want target-based orbit and pan. Choose Free camera when no molecule should hold the view: drag empty viewport space to look, use W/A/S/D to translate, Q/E to move down/up, and the wheel to dolly. With the viewport focused, arrows look around and Page Up/Page Down or +/− dolly; Shift makes a finer step. The on-screen touch pad mirrors movement on touch devices. Press K to key the current view.
Choose Orbit again for an obvious route back to target-based navigation. Orbit and Free camera control how you travel while authoring; Focus viewport only changes the workspace layout, while tracking, focus and depth of field are editable shot outcomes.
Focus viewport keeps the essential tool strip while hiding the cast, question panel and timeline; Restore workspace or Esc returns them. On a narrow screen, Cast and Timeline are drawers. Tap to select, long-press without moving for the context menu, then touch-drag to preview and release to fix a requested pin. Keyboard users move the visible point-picking crosshair with arrows and press Enter; the hovered component and scientific site are announced.
Point pins, hinge cues, destination ghosts, growth previews, reaction marks and camera frames persist across the handoff. Cancel or Esc exits a picker without writing records. Shape Lab becomes a stacked full-screen editor, with a horizontal tool row and two-finger pan/zoom.
Shape Lab’s Draw tool is a general 3D authoring gesture, not a helix preset. Drag an arbitrary centreline and choose Solid stroke, Ribbon or a Twisted bundle of 1–12 strands. Optional physical cross-links follow the same route. Snap start to visible surface starts on the shown mesh; hold Shift + wheel or change Depth plane (Å) while drawing to move through 3D. Choose Blend, Fuse, Cut or Start fresh for how the form joins the graph.
Completed paths expose editable handles. Use Continue from end, Reverse selected path or add another stroke to branch; Delete selected removes the whole logical form and Undo/Redo restore it. Clear canvas provides a blank canvas, while primitive layers remain available. The latest editable working draft is saved and restored locally for this project after an interruption.
Pull, Push, Inflate, Smooth and Flatten the visible mesh with Radius (Å), Strength, Soft edge and optional Mirror X/Y/Z symmetry. One drag is one reversible brush layer. Right/Alt-drag or Orbit turns the object; middle-drag, Pan or Shift while navigating moves it; wheel/pinch zooms and two-finger touch also pans. For Paint regions or Binding ports, press Pick surface point and click or tap once; the cyan pin persists without sculpting. Press Live preview while iterating, then choose Final or Ultra under Mesh quality and Build mesh. Export asset downloads either the editable .molasset master or a baked full-Final OBJ without adding it to the scene. Add to scene is the separate explicit install action; the actor remains labelled Illustrative geometry.
Finish → Audio and narration imports local sound, draws its waveform and exposes Timeline start, trims, gain, mute and fades. Add cue markers and export shot captions/labels as SRT or VTT. Audio bytes live in ProjectStore assets, not as base64 in the working document.
Use Save now, browser revisions and Export project before clearing site data. Your Molstudio account also keeps a private project copy in sync across devices. Still and animation dialogs independently include or omit annotations. H.264 MP4 is preferred; native MP4 then WebM are browser fallbacks, and authored audio is mixed only where the browser/codec reports support.
Open AI Director, scope its Context preview to the project, current selection or current shot, then describe the visible outcome. Connect through a Direct browser endpoint, use universal Copy / paste, or enable an Origin-scoped window bridge for one trusted companion page. Each route receives the same compact scene brief.
The model returns a molstudio.llm-plan/1 plan. It can begin with project.blank, import through structure.import_rcsb, structure.import_file or structure.import_url, construct an illustrative asset with shape.create, and remove an exact cast member with asset.remove. A local import exposes Choose file; assembly alternatives remain a visible choice. Blank and remove also require their literal safety token and a separate destructive confirmation.
Nothing changes until explicit Apply. A mixed plan first shows Apply construction; after it completes, Molstudio refreshes the sanitized context and revalidates every remaining actor reference before showing a second, scene-only Apply scene edits. A later top-level ID field can refer to a new entity as $result.<stepId>.actorId (or the documented component, selection, asset or generic ID suffix); it cannot interpolate that token into prose, URLs or nested records. If construction is the final stage or the scene continuation cannot proceed, Undo imported/build stage restores the pre-stage project; the separately applied atomic authored scene edit has Undo this plan while newest. Read the complete AI Director safety and connection guide.
The brief excludes raw App data, atom coordinates, PDB/mmCIF text, trajectories, meshes, audio, filenames, credentials and the internal creator bridge. Prerequisite results expose sanitized IDs, never source or mesh payload. Direct endpoint calls require HTTPS (except localhost) and browser CORS; some providers block this path. A token is browser-visible, stays in memory by default and can only be retained for the browser session by explicit choice. Use Copy / paste or a browser-safe relay instead of exposing a long-lived provider key.
Model-directed structure URLs are limited to credential-free HTTPS RCSB or AlphaFold locations and still depend on browser CORS. Other sources go through the visible local-file chooser. Exact surface contacts, cartoon residue envelopes, flex regions and camera composition remain viewport handoffs. The model can open those guides, but cannot invent a binding pose, affinity, folding pathway or surface hit. Static /api/ GET files describe the tools and schema; they are not a live HTTP control API.
The WebGPU hybrid badge means supported residue-bounds and contact-field compute are ready; the production visual renderer still uses parity-complete WebGL2. Unsupported, insecure or lost devices stay on WebGL2 compatibility without blanking the live canvas. Click the badge to toggle WebGPU-first/off and inspect its tooltip.
Guided choreography, procedural units, Shape Lab geometry, staged contacts and physical ripples are illustrative unless backed by imported simulation data. A two-state morph is interpolation, not a physical path. DCD/XTC or multi-model playback uses imported frames but does not unwrap periodic coordinates. Deposited atoms remain unchanged.
Rendered studies · eight editable scenes
Eight films use eight shot languages, including cartoon and molecular-surface treatments of one complete replication fork, but every cue is made from the same editable components, behaviours, paths and relationships available in the studio. Play a cut, then pull it apart.
T7 replisome · mechanistic composite
The parental duplex meets a T-shaped fork rather than passing through gp4: the leading template peels outside toward one gp5–thioredoxin polymerase while the lagging template enters the gp4 central channel and reaches the other. Continuous leading synthesis runs beside a four-nucleotide T7 primer, lagging loop growth and release, and two emerging daughter duplexes.
T7 replisome · actor-local molecular surfaces
The same asymmetric fork choreography is restaged through hydrated molecular surfaces, active-site cutaways, and restrained contact waves. The leading template remains outside gp4 for continuous synthesis; the lagging template enters its central channel for four-nucleotide priming, looped discontinuous synthesis, and release.
DNA synthesis · processive strand growth
Twenty incoming dATP copies share one constrained solvent-to-pocket route and hand their conserved atoms to a monotonic daughter strand. DNA advances by the deposited D11→D12 helical transform per addition while the polymerase remains the stable visual hub.
DNA synthesis · retained chain growth
The complete deposited seven-base primer remains visible while each dATP follows one continuous route, pauses in the seated pose and hands off in place to a retained unit. Four additions and three restrained translocation beats produce an explicit eleven-base primer.
DNA polymerase · hydrated molecular surface
A clipped molecular surface exposes the active-site cleft as the selected domain opens, admits the staged nucleotide, and closes around its deposited pose.
Kinase recognition · ghosted surface + ligand space-fill
Track AQ4 into the EGFR cleft, hold at its deposited 1M17 pose while the contact shell resolves, then release along a second independently editable path.
DNA processing · cartoon silhouette + luminous DNA
A locked profile separates clamp and cargo: close, advance the duplex 3.4 Å, then reopen, repeating in three discrete, independently editable beats.
Kinase communication · cartoon map + residue bands
A contact cue at deposited AQ4 travels through four authored residue bands toward the distal lobe, turning a static structure into a clear explanatory signal map.
Move, rotate, change depth, scale, and sketch paths in the frame with pointer or touch. A gesture is one undoable edit; Auto-key records the current playhead, while dragging without it adjusts the whole setup. Right-click, touch long-press, or Shift+F10 opens the selection-aware viewport menu. Small commands act in place; route, exact-contact, flex, growth, appearance and camera outcomes open the corresponding full Director workspace with the clicked surface site retained.
Reuse any rigged molecular selection as retained numbered geometry in a port chain, editable curve/path polymer, helix, cyclic ring, dihedral pair, hex sheet, 3D lattice, spherical shell, filled volume, or radial spokes. The curve layout places units at even arc-length intervals along editable control points, can key the path through time, and can lock contour length while a DNA loop changes shape. Count, dimensions, spacing, orientation, timing and event responses remain editable; each unit stays directly selectable and keyable. One deterministic Variation & Shaping layer adds seedable position and rotation jitter, taper, bend, and adjustable waves to every spatial layout without additional draw calls. Port chains retain exact connector continuity. Reveal or hide already-loaded geometry when that is the intended effect; isolate actors, track focus, and anchor timed labels that survive export. Procedural layouts are authored construction rules, not assembly or conformation predictions.
Behaviours repeat in phased cycles; components generate time-offset copies; and any component can approach, dock, bind to, follow, or release from any other. Arrival and release can start another ordinary behaviour, so one interaction can drive the next step of the machine.
Resolve a one-letter protein or nucleic motif, deposited residue range, ligand name, component ID, or molecular formula against one chosen component. The result is an exact insertion-code-aware saved selection, even when a motif occurs more than once, and it can immediately become a rig, a visible contact target, a framed shot, an illustrative hinge, or the scope of a matched deposited-state morph. Formula labels distinguish source metadata containing hydrogen from formulas computed over displayed heavy atoms. This is scientific addressing of known coordinates, not folding prediction, docking energetics, affinity scoring, or molecular dynamics.
Let Dock or Bind send a damped soft-impact ripple from the contact through the receiving molecule. The packet physically displaces ribbons, molecular surfaces, atoms and sticks in ångströms; signed tint, roughness and micro-normal travel on that same moving surface. Geometry amplitude, material intensity, colour and authored duration are editable, while emissive glow is a separate optional layer. Or add a contact flash, molecular ripple, energy arc, or particle burst at any actor or named contact. These deterministic cues render into finished films and remain clearly marked as illustrative rather than molecular dynamics.
Load a second PDB or mmCIF state to chemically match and rigidly align atoms before an explicitly interpolated morph, or play frames from multi-model PDB/mmCIF, standard 32-bit-record DCD, or XTC directly. Binary files use the selected component’s displayed, filtered heavy atoms as their companion topology and require that exact atom count and trajectory file order; all-atom files with hydrogens or solvent need a matching filtered topology. Source timestamps remain provenance while the authored clip spaces frames uniformly. Periodic coordinates are not unwrapped or made whole, so prepare wrapped trajectories before import. Atom representations move per atom; ribbons and surfaces follow residue-averaged deformation. Source coordinates remain unchanged, and interpolated frames are never presented as a physical pathway.
The example constructions are conveniences rather than fixtures. Each one compiles to the same editable component graph you would build by hand, and each stays optional. Take one apart to see how it works, then rebuild it your way.
Axes and pivots derive from the selection itself, such as a helix axis or a hinge, or they float free where you place them. The geometry of the data guides the motion without limiting it.
All motion lives in the client-side project document. Deposited atom coordinates remain unchanged, and provenance labels keep demonstration clearly separated from evidence.