sergeinikolenko/burette/preview-molecular-structures

Preview molecular structures

Use Burette for bounded molecular inspection and transient chemical sketching.

Choose the tool

• Use preview_molecular_file when the user provides one supported molecular

structure attachment.

• Use preview_pdb_structure only when the user explicitly names a

four-character PDB ID or clearly asks to open that public PDB entry.

• Use render_molecular_scene when the user asks to select or focus a typed

chain, residue range, or component; clear a selection; reset the camera; or hide/show polymers, ligands, ions, or water. Pass the same PDB ID or authorized attachment again because the public server does not retain widget sessions. When the source and selector are supplied, call this tool directly once: it loads the structure and applies the actions, so a preliminary preview is unnecessary. Do not split opening, selecting, focusing, and hiding waters across multiple cards.

• Use open_ketcher when the user asks to draw or edit a small chemical

structure in the hosted widget. Seed only bounded inline KET, MOL, RXN, or SMILES content when it is supplied.

• Use control_ketcher for a follow-up Ketcher action. First use the current

surfaceId and structureRevision from the editor snapshot; send a revision-checked set_structure, clear_structure, highlight_atoms, or get_structure action. request_persist only reaches a user-confirmation boundary and never writes silently.

• If several supported attachments are present and the target is unclear, ask

which single structure to open.

• If no structure is identified in this conversation, ask for an attachment or

PDB ID before any molecular call. Do not borrow an identifier from another chat, a cached widget, a suggested demo, or earlier unrelated activity.

Present the result

1. Call the selected tool once with the user's attachment or PDB ID.
2. Report the bounded composition summary returned by the tool. Do not infer

counts that are absent from the result.

1. Let the interactive Burette preview carry the detailed 3D inspection.

The user can rotate, zoom, select residues, inspect the sequence, change representations, and use measurements directly in the result.

1. State format limitations or parser notes when the result includes them.
2. Treat burette.activeSelection from widget context as the user's current

selection only when its source matches the structure explicitly opened in this conversation. Tool-returned data and a prepared scene are not a loaded view. Do not say “done”, “selected”, “focused”, or “hidden” until the widget reports those applied actions. If there is no acknowledgement, explicitly state that rendering/application is unconfirmed, not completed.

Boundaries

• For unsupported docking, affinity, simulation, or local overwrite requests,

explain the limitation without opening a preview as a substitute. Offer inspection separately; a PDB ID in a docking request is not an inspection request.

• Do not claim that this public plugin edits, overwrites, or deletes molecular

source files. Ketcher edits exist only in the ephemeral hosted widget relay.

• Do not claim local macOS app control, docking, simulation, structure

prediction, or remote job execution. Those are outside this hosted plugin.

• Do not treat a molecular preview as medical diagnosis, clinical advice, or

proof of biological function.

• Do not request credentials, private URLs, local paths, health records, or

other sensitive identifiers.

• Files larger than 3 MiB or unsupported formats need a smaller supported

structure file.

• Arbitrary residue isolation and persistent representation overpaint are not

available in the hosted action allowlist.