01 / Structure Interrogate coordinates Selections and measurements retain stable atom addresses and the coordinate state used.
Selection builder Atom, residue, chain, entity and spatial logic Local · structure required Measurements Distance, angle and dihedral objects Local · structure required Contacts + H-bonds Explicit rules, cutoffs and atom pairs Local · structure required Superposition + RMSD Matched atoms, transformation and residuals 2 structures required
02 / Sequence Map residue identity Sequence, observed coordinates and missing regions remain distinct but linked.
Sequence ↔ structure map Chain numbering, insertions and missing coordinates Local · polymer required Pairwise alignment Parameters and gaps retained with the result Local · 2 sequences Multiple alignment Bounded progressive alignment with retained parameters Built in · local Database search RCSB MMseqs2 sequence search with retained alignments Built in · RCSB
03 / Analyse Quantify structure Geometry and surface results are recorded as calculations, never inferred from appearance.
Validation Local coordinate screen plus deposited PDBe report Built in · local / archive Ramachandran plot Linked residues and calculated φ/ψ values Local · protein required Surface area SASA with probe radius and selection recorded Local · structure required Cavities + pockets Enclosed voids locally; energetic pocket evidence labelled separately Built in · local geometry
05 / Model + edit Create derived coordinates Edits create a derived state. They never overwrite deposited or predicted source coordinates.
Mutate residue Choose rotamer and preserve the unmodified parent Local proposal Hydrogens + bond order Validate valence and generate explicit preparation hypotheses Built in · local Relax / minimise Bounded local mechanics with restraints and convergence record Built in · local Loop + side-chain model Generate and rank explicit local candidate states Built in · local Predict or retrieve structure AlphaFold DB lookup or zero-config ESMFold inference Built in · archive / service
06 / Ligands + docking Examine molecular recognition Observed poses, hand placement and calculated docking poses are labelled separately.
Ligand contacts Explicit geometric atom pairs and cutoffs Local · ligand required SMILES + ligand builder Paste SMILES, review its graph, add it as an object and dock locally Built in · local Dock ligand Deterministic bounded pose hypotheses in a reviewed search box Built in · local Protein / peptide docking Rigid-body local pose hypotheses from an explicit mobile selection Built in · local
08 / Compute Run local scientific compute Built-in browser engines produce explicit baseline results. Optional providers may accelerate or replace a method after review.
Built-in compute ready Local minimisation, short dynamics, electrostatics, pose hypotheses, loops and density fitting require no account, server or executable.
Molecular-mechanics energy Inspect the declared local energy terms without changing coordinates Built in · local Relax / minimise Restrained bounded minimisation into a reversible derived state Built in · local Short molecular dynamics Seeded local Langevin trajectory with complete parameters Built in · local Optional accelerator / specialist engine Review endpoint, capability and any data leaving this browser Optional Compute job history Input hashes, parameters, engine versions and outputs No jobs Electrostatics Local point-charge field with declared dielectric and charge source Built in · local Dock ligand Seeded bounded pose hypotheses against the current receptor Built in · local Dock protein / peptide Rigid-body pose hypotheses from explicit objects or selection Built in · local Model a loop Seeded candidate backbone hypotheses with explicit limitations Built in · local Fit to density Restrained real-space fitting to the open map Built in · map required
09 / Scripts + batch Make operations repeatable Commands target stable identifiers and enter the same revision history as graphical actions.
Command surface ready Use the query bar below for selections and commands. Execution begins only when a compatible command engine is loaded.
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Command reference Discover available local commands and exact arguments Local Batch workflow Preview every target and operation before atomic local execution Built in · local Export command record Readable settings, display operations and project history Project required
10 / Reports Communicate evidence Reports separate source facts, calculated results, warnings and visual presentation.
Analysis report Results, methods, units, parameters and coordinate lineage Results required Provenance manifest Sources, hashes, archive revisions and derived states Project state Export coordinates Choose original or a named derived coordinate state Structure required Send to Molstudio Transfer scientific state into the cinematic renderer Structure required
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No calculated results
Measurements, alignments and analyses appear here only after successful execution. Opening a tool does not create a result.