Help & Documentation

Appearance

Tools Panel ​

The Tools Panel is a vertical toolbar on the right side of the interface providing access to interaction tools. From top to bottom:

  • Pointer Tool — Hover over atoms to display information.
  • Measurement Tool — Create distance, angle, and dihedral measurements.
  • Selection Tool — Use 3D space to create and edit selections.
  • Builder Tool — Build and edit molecules in 3D.
  • Torsion Tool — Rotate bonds to adjust molecular conformation.
  • Download from RCSB — Import structures directly from the RCSB Protein Data Bank.
  • Open MARA — Launch the MARA representation agent.

Selection Tool ​

The Selection Tool allows you to create selections by clicking on or dragging over atoms in 3D space. Selection granularity options include:

  • Select by chain — Select entire chains.
  • Select by residue — Select individual residues.
  • Select by atom — Select individual atoms.

The Selection Panel shows information about the current selection (entry count, chains, residues, atoms) and provides:

  • Clear — Clear the current selection.
  • Create — Create a new component from the current selection.
  • Update — Update the current component with the current selection.

Measurement Tool ​

The Measurement Tool creates measurements by selecting atoms in 3D space. Measurement types include:

  • Measure distance — Measure the distance between two atoms (displayed in Ångströms).
  • Measure angles — Measure the angle between three atoms (displayed in degrees).
  • Measure dihedral — Measure the dihedral angle between four atoms (displayed in degrees).

Each measurement appears as a row in the Measurements Panel with a delete button to remove individual measurements. Hovering over a measurement row in the panel highlights that measurement in the 3D view.

Builder Tool ​

The Builder Tool enables 3D molecular construction and editing. Upon activation, you can choose to:

  • Create a new structure — Start building a new molecule from scratch.
  • Edit this structure — Select an existing ligand to modify.

The Builder Panel provides the following modes:

  • Atomic draw mode — Place individual atoms. Geometry options determine the number of dummy bonds: Linear (one), Trigonal (two), or Tetrahedral (three).
  • Draw by group — Insert pre-built groups from categories including: Recent, Atoms, Rings, R Groups, Amino Acids, BioMolecules, and Functional Groups.
  • Add bond — Create a bond between two existing atoms.
  • Replace atom — Swap one atom type for another.
  • Delete an atom — Remove atoms from the structure.
  • Disable builder tool — Exit the Builder Tool.

Available Atoms: Hydrogen (H), Carbon (C), Nitrogen (N), Oxygen (O), Fluorine (F), Phosphorus (P), Sulfur (S), and Chlorine (Cl).

Minimization ​

The gear icon beside Minimize opens the force field settings:

  • Force Fields — Choose the force field used for minimization: MMFF94, MMFF94s, or UFF.
  • Number of steps — Set how many minimization steps to run (e.g., 200).

Click Apply to confirm, or Cancel to dismiss.

While in the Builder Tool, clicking Minimize runs a force field minimization on the structure. After minimization completes:

  • The minimization energy is displayed (e.g., 46.6 kJ/mol).
  • Undo/Redo buttons allow you to step through edits made while building or editing a molecule.

When saving, the options depend on your starting point:

  • Starting from Create New — Save as new ligand.
  • Starting from an existing ligand — Save as new ligand, or update the original ligand.

Torsion Tool ​

Video: Torsion Tool (Beta) ​

The Torsion Tool rotates bonds to adjust the conformation of a structure. Select a structure in 3D space, or use the list in the panel to choose what to edit:

  • All Chains — Edit all residues for all chains in a workspace.
  • All Ligands — Edit all ligands in a workspace.
  • Chain A — Edit all residues for a single chain.
  • A:50D_501 — Edit an individual ligand.

Structures switch to a ball-and-stick representation on entering the Torsion Tool, and return to their previous representation on exit.

To rotate a bond, hover over one half of it and pull the trigger. A Show torsion for the entire molecule option displays torsions across the whole structure. Undo/Redo step through changes, Save commits them, and Cancel discards them.