Executes a single PyMOL command given in literal PyMOL syntax.

NOT a natural-language interface. user_input is matched against a fixed table of command patterns; anything else is rejected rather than guessed at. Translate the user's request into PyMOL syntax yourself, then call this once per command. Use list_commands to look up exact syntax.

instance is the port of the PyMOL to drive. Leave it unset when only one is running. With several running an unset instance is an error rather than a guess, since driving the window the user is not watching looks exactly like the command doing nothing. Call list_instances to see the choices.

Translating requests: "Load PDB 1UBQ and show it as cartoon" -> parse_and_execute("fetch 1ubq") -> parse_and_execute("as cartoon, 1ubq") "Colour chain A red" -> "color red, chain A" "Show sticks for residues 1-50" -> "show sticks, resi 1-50" "Open /data/model.pdb" -> "load /data/model.pdb" "Select the binding site" -> "select site, byres (polymer within 5 of ligand)"

Common mistakes:

• Multiple commands in one call. "fetch 1ubq and show cartoon" fails; the whole string is read as one filename/code.

• load for a PDB ID. load takes a file path; use fetch for a 4-character accession code like 1ubq.

• Selections as prose. Write show cartoon, chain A, not show cartoon for chain A -- the selection is a second argument after a comma.

• Conversational filler. "please show cartoon" does not match; send "show cartoon".

Selections use full PyMOL algebra (chain A and resi 1-50, not solvent, byres (... within 5 of ...)). Commas separate arguments, so a selection containing a comma must be rewritten with + (resi 1+2+3).

Returns PyMOL's output, or a message describing the parse/execution failure.

Lists the running PyMOL instances and what each has loaded.

Each PyMOL claims its own port, so several can run at once. Pass a port as instance to parse_and_execute to drive that specific one. Use this when a command reports the choice is ambiguous, or when the user refers to a particular window.

The loaded object names are what distinguish one window from another; a port number on its own identifies nothing to a human.

Lists the PyMOL commands parse_and_execute accepts.

Without filter, returns every command name with a one-line description. With filter (a substring matched against names and descriptions), returns full detail for the matches: the exact regex the input must satisfy, plus each parameter's name, whether it is required, its default, and its allowed values. Use it to confirm syntax before calling parse_and_execute.

Examples: filter="color" for the colouring commands, filter="cartoon" for cartoon-related ones, filter="fetch" for the exact fetch signature.