Table of contents# Welcome What’s New in Avogadro 2 Major New Features Interface Changes Getting Started Introduction Drawing Molecules Making Selections Tools Navigate Tool Draw Tool Bond-Centric Manipulate Tool Manipulate Tool Selection Tool Auto-Rotate Tool Auto-Optimize Tool Measure Tool Align Tool Menus File Menu Edit Menu View Menu Build Menu Select Menu Extension Menu Building Molecules Importing Molecules by Name Importing from the Protein Data Bank (PDB) Building a Peptide Building DNA or RNA Building Carbon Nanotubes Insert Molecular Fragments Building with SMILES Building Materials Building a Supercell Making a Crystal Surface Slab Building a Polymer Unit Cell Perceiving Crystall Symmetry Reducing Crystals to a Primitive Unit Cell Scaling Crystal Cell Volume Building Molecule-Surface Interactions Optimizing Geometry Introduction to Molecular Mechanics Finding Conformers of Molecules Geometry Constraints Display Types Different Display Styles Coloring Part of a Molecules Tutorials Naming a Molecule Viewing Vibrations Viewing Molecular Orbitals Viewing Electrostatic Potential Maps Using QTAIM (Atoms in Molecules) Analysis Extensions ABINIT Input Generator LAMMPS Input
