Molecules in Catalyst

How do I . . .

• Build and edit molecules
  • Build a molecule?
  • Build a peptide?
  • Create a molecule by copying and pasting SMILES strings?
  • Atoms
    • Add an atom?
    • Select atoms or bonds?
    • Deselect atoms or bonds?
    • Change the element of an atom?
    • Create a negative ion?
    • Create a positive ion?
    • Neutralize an ion?
    • Delete atoms or bonds?
  • Bonds
    • Add a bond (close a ring)?
    • Change the type of a bond?
    • Aromatize a ring?
    • Change the 2D drawing style of a bond?
  • Stereochemistry
    • Change stereochemistry?
    • Invert the stereochemistry of a bridgehead atom?
    • Flip a ring atom?
    • Rotate a bond?
• Refining the structure
  • Clean a 2D structure?
  • Generate a standard 3D structure?
  • Orient a 3D structure to its 2D structure?
  • Minimize a molecule?
  • Measure interatomic distances?
• Conformers
  • Generate a conformational model?
  • Display individual conformers?
  • Save conformers?
  • Delete a conformer?
  • Compare two molecules?
• Display
  • Display hydrogen atoms?
  • Display atom labels?
  • Display stereochemistry labels?
  • Display compound names?
  • Display 2D molecules in monochrome?
  • Choose the display style for 3D molecules?
  • Specify the color of selected parts of a molecule?
  • Specify view and style attributes for selected objects in the workspace?