Structure Manipulation

Basic Controls

Action Windows Controls Mac/Unix/Linux Controls
Rotate Display Left-click & drag Left-click & drag
Zoom Display Shift-left-click & drag or Mousewheel Shift-left-click & drag or Mousewheel
Pan Display Ctrl-left-click & drag Mousewheel click & drag
Change Binding Site Radius Ctrl-Mousewheel Cmd(Mac Command Vector SVG Icon (3) - SVG Repo)-Mousewheel
Select Atoms Left-click atoms Left-click atoms
Expand Selection Left-click selected atoms Left-click selected atoms
Modify Terminals Right-click atoms Right-click atoms
Search Fragment Maps For Substitutions Right-click atoms (Ctrl reverses dir) Right-click atoms (Cmd(Mac Command Vector SVG Icon (3) - SVG Repo) reverses dir)

Hot Keys

  • H: Momentarily display all compound hydrogens
  • L: Zoom to Ligand view or view the next compound
  • R: Momentarily highlight functional groups
  • X: Hide the active compound momentarily
  • W: Show weak hydrogen bonds (green bars) momentarily (These will not show when "Protein View" or "Hide all hydrogens." are selected. )  
  • D: Display default docking box
  • V: Momentarily display all "Growable Vectors" (Clay Pink) and "Growable and Replaceable Vectors" (Clay Blue)
  • ←,→/↑,↓: View previous, next compound


The Query Selector button allows the user to provide a query using one of several common specifiers or compound and protein specific specifiers to select derived atoms, residues, ligands, chains, or proteins. Remember that changing View, clicking in the background, or submitting another query will remove the selection.

The select command takes an expression formed by combining primitives with 'and', 'or', or 'not', nested with parentheses.

Selection primitives are: Note the lower case
all, none, file, selected, visible, selection, protein, solute, hetero, dna, rna, sugar, saccharide, sugars, saccharides, model, model-number, model-numbers, chain, chains, residue, ligand, fragment, sketch-group, sketch, compound, residues, ligands, fragments, sketch-groups, compounds, water, crystal-water, waters, crystal-waters, atom, atoms, atom-set, atom-sets, atom-type, atom-types, hydrogens, element, elements, atom-obj, sketch-obj, sketch-group-obj, fragment-obj, ligand-obj, residue-obj, snapshot-obj, solute-obj, subset, within.

It is important to remember that "atoms" are given names according to Amber naming conventions so selections like all carbons may require multiple carbon specifications. "element" will select all of a given element.

Examples - Selection in pink:

To select compounds associated with the protein: ligand

Compound/ligand name: K26