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()-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() 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
Query
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