ChimeraX docs icon

Toolbar: Molecule Display

Icons in the Molecule Display tab of the Toolbar allow changing the display of atomic models with a single click. They apply to the displayed models only (those with  eye icon  checkboxes in the Model Panel checked for themselves and any parents), and if those models contain a selection, only the selected parts. See also: Actions menu, Presets menu, Basic Actions, making images

Clicking an icon shows the executed command in the Log. Molecule display icons act on the currently selected atoms, if any (specified as sel), otherwise the currently displayed atomic models (specified as a list of model numbers). There may be alternative commands for performing the same action.

icon description command(s)
show atoms/bonds show
hide atoms/bonds hide
 show biopolymer ribbons (cartoons) show ribbons

(same as cartoon)

hide biopolymer ribbons hide ribbons

(same as ~cartoon)

show molecular surface show surfaces

(same as surface)

hide molecular surface hide surfaces

(same as surface hide)

stick-style atoms/bonds style stick
sphere-style atoms style sphere
ball-and-stick atoms/bonds style ball

nucleotide styles (more in Nucleotides tab)

  • atoms/bonds (no abstraction)
  • filled rings
  • tube/slab
  • ladder

nucleotides atoms; style nucleic stick

nucleotides fill; style nucleic stick

nucleotides tube/slab shape box

nucleotides ladder

color-code heteroatoms by element color byhetero
color-code chains by chain ID color bychain
rainbow-color chains blue → red rainbow
color molecular surface by Coulombic electrostatic potential coulombic
color molecular surface by hydrophobicity
(molecular lipophilic potential)
color by B-factor color bfactor
color-code nucleic acids by residue type color bynucleotide
show hydrogen bonds hbonds
remove all hydrogen bonds ~hbonds
show unique sequence(s) (none, but see sequence chain)
show chain-interface network interfaces ~solvent

UCSF Resource for Biocomputing, Visualization, and Informatics / August 2020