command-reference.md

MolCompose command reference

Every molcompose command, its arguments and what it returns.

Arguments in bold are required; the rest are keywords with defaults. Every command writes itself to the ChimeraX Log, so any analysis can be replayed.

26 commands.

Command	Category	Arguments	Does
molcompose	Structure Analysis	—	List the MolCompose commands
molcompose affinity	Structure Analysis	model object, temperature float	Predict binding free energy and Kd (PRODIGY IC-NIS)
molcompose blocks	Structure Analysis	model object	List the four named parts of a characterised complex
molcompose buriedarea	Structure Analysis	model object	Buried surface area of the detected interface
molcompose capabilities	Structure Analysis	model object, predictor string, paeFile string	Report which analyses this structure supports
molcompose characterise	Structure Analysis	group_a, group_b, model object, distance float, criterion string, style bool	Run the full interface characterisation in one call
molcompose color by	Depiction	metric, model object, statistic string, scope string	Colour residues by a per-residue metric
molcompose confidence	Structure Analysis	model object	Report pLDDT, ipLDDT, and pDockQ for a predicted model
molcompose contacts	Structure Analysis	model object, off bool	Show close contacts across the detected interface
molcompose ddg	Structure Analysis	path, interfaceOnly bool, model object, format string, statistic string, top int	Load predicted mutation effects (ΔΔG) from a predictor
molcompose dockq	Structure Analysis	reference, model object, chainMap string	DockQ and CAPRI components against a reference complex
molcompose energy	Structure Analysis	path, chains string, model object, top int, solvation string	Load a per-residue MM/PBSA decomposition
molcompose export	Depiction	path, width int, height int, supersample int, transparent bool, saveSession bool, overwrite bool, dpi int, saveRecipe bool, keyFontSize int	Export a publication image, with print resolution, and optionally the session and command recipe
molcompose flexibility	Structure Analysis	path, chains string, model object	Load per-residue RMS fluctuation from a trajectory
molcompose focus	Depiction	target string, model object	Fit the view to a model or detected interface
molcompose hbonds	Structure Analysis	model object, off bool	Show hydrogen bonds across the detected interface
molcompose hotspots	Structure Analysis	metric string, model object, minArea float, top int	Rank interface residues by buried surface area
molcompose interactions	Structure Analysis	model object, types string, off bool, saltBridge float, hydrophobic float, piStacking float, cationPi float	Detect typed non-covalent interactions across the interface
molcompose interface	Structure Analysis	group_a, group_b, model object, distance float, criterion string	Detect an interface between two protein chain groups
molcompose interface all	Structure Analysis	model object, distance float, criterion string	Detect every contacting protein chain pair
molcompose ipsae	Structure Analysis	path string, model object, paeCutoff float, predictor string	ipSAE interface scores from a prediction PAE file
molcompose report	Structure Analysis	path, model object, format string	Write a complete interface characterization report
molcompose reset	Depiction	model object	Reset a model to the MolCompose neutral baseline
molcompose seqcolor	Structure Analysis	path string, model object, source string, statistic string, load bool	Export the per-residue colouring as SCF for the Sequence Viewer
molcompose source	Structure Analysis	name	Declare who issues the next command, for the recipe's source attribution
molcompose style	Depiction	preset, model object, labels int, rankBy string, references string, align string, partner string	Apply a versioned MolCompose visual preset

Reading the table

model defaults to the only open structure, or must be given when several are open. Commands that need an interface will say so rather than guessing: run molcompose interface first, or molcompose characterise, which runs the whole battery and names anything it could not compute.

Nothing here needs network access, and no command estimates a metric whose assumptions the structure does not satisfy — a confidence score asked of a crystal structure is reported as skipped, by name.