Load a molecular structure or single-frame coordinate file into PyMOL.

Returns the created object name and its atom/state counts.

Fetch a structure from the RCSB PDB (requires network) and load it.

List all loaded object names in the current PyMOL session.

Return atom count, state count, and chains for a loaded object.

Reinitialize PyMOL, clearing all objects, selections, and settings.

Ray-trace the current scene to a PNG and return it inline.

[opt-in] Execute raw PyMOL command-language statements. Requires PYMOL_MCP_ALLOW_CODE_EXEC=1.

[opt-in] Execute a Python snippet with PyMOL cmd in scope. Requires PYMOL_MCP_ALLOW_CODE_EXEC=1.

Create a named selection and return how many atoms it matched.

Summarize a selection: atom count, chains, and residue names present.

Show (or exclusively set with only=True) a molecular representation for a selection.

Hide a representation for a selection.

Color a selection.

Color a selection along a spectrum of a per-atom expression (e.g. B-factor).

Set the render background color.

Orient the camera along the principal axes of a selection.

Zoom the camera onto a selection.

Rotate the camera about an axis.

Measure the distance (Angstroms) between two single-atom selections.

Measure the angle (degrees) defined by three single-atom selections.

Measure the dihedral (degrees) defined by four single-atom selections.

Sequence-align and superpose mobile onto target (use for different structures).

Save a selection/session to a file (format from extension).

Load a GROMACS/DCD trajectory: load the structure, then append frames as states.

Requires matching atom count/order (trjconv strip/reorder is the common pitfall).

Load any MDAnalysis-readable trajectory (LAMMPS dump, AMBER NetCDF, ...) by injecting coordinates into PyMOL states. Requires the optional md extra (MDAnalysis).

Compute the F3 or F4 water order parameter for a clathrate-hydrate system.

F4 ~ 0.7-0.95 = hydrate, ~0 = liquid, ~ -0.4 = ice Ih. F3 <= 0.04 = hydrate-like.

Build the water hydrogen-bond network and report coordination statistics.

A well-formed clathrate framework has ~4 H-bonds per water (tetrahedral).

Classify water molecules as liquid, ice, or hydrate with CHILL+.

The result contains the six class counts, per-water classes, fractions, and the unique O-O cutoff network in water input order.

Identify clathrate cages (TRACE): ring perception -> cage assembly -> face-count typing.

Returns per-type cage counts (5^12, 5^12 6^2, 5^12 6^4, ...) and the overall structure (sI / sII / sH). Validated: sII -> 128x 5^12 + 64x 5^12 6^4; sI -> 16x 5^12 + 48x 5^12 6^2.

Compute clathrate cage occupancy: assign guest molecules to detected cages (one per cage).

Draw each detected cage as a wireframe polyhedron — cylinders along the O-O ring edges plus spheres at the water-oxygen vertices, colored by cage type (5^12=cyan, 5^12 6^2=violet, 5^12 6^4=red, ...). Builds a single CGO object named cages for render_image.

Draw the classified CHILL+ O-O network as a colored CGO object named chill_plus.