Some relevant Jmol commands

A very basic introduction; for full details, see the Jmol Scripting Documentation.

To select atoms


This is not a command, but a keyword for an "atom expression". Typically used in the select command.

It refers to the set of atoms identified by Jmol to be part of a protein (due to their chemical structure containing the key atom names).


This is also a keyword for an atom expression. Typically used in the select command.

"Ligand" is the set of atoms that

  • are not part of a protein or a nucleic acid
  • are not water

Be cautious; it will not always select what you may think are "ligands". For example, monoatomic ions (Ca2+) are part of the ligand set, while isolated nucleotides like GMP will be identified as nucleic and hence not ligand.


An essential command, as any style of rendering that you want will apply only to the set of atoms that is selected at that moment.

  • select all
  • select ligand
  • select 33,36,37 ; residue numbers in a chain
  • select Cys ; cysteine residues
  • select _Zn ; zinc atoms


Most frequently employed as part of a select command. It has several variants or uses; among them:

  • belonging to same group or residue:
    select within(group, _Mg) ; all atoms in the same group as a magnesium atom
    select within(group, atomNo=87) ; all atoms in the same group as atom number 87
  • by distance:
    select within(3.0, atomNo=87) ; all atoms at 3 angstroms or shorter distance from atom number 87
    select within(2.8, [ATG]) ; all atoms at 2.8 angstroms or shorter distance from any atom that belongs to the group(s) named "ATG"

combination: and, or, not

  • select protein and _N
  • select protein & _N
  • select protein and not _C
  • select protein & ! _C
  • select _Ca or _Mg
  • select _Ca , _Mg

To specify rendering style


Applies a color to the selected atoms, their bonds and other graphic elements attached to them.

  • color yellow ;
  • color [xFFAA00] ; red, green, blue components
  • color [255,200,0] ; red, green, blue components
  • color structure ; color proteins by type of secondary structure
  • color group ; color macromolecules by the order of residue in the chain
  • color chain ; color each macromolecule chain in one color (good to find out the nr. of subunits we have)


Sets the thickness of a stick representing a bond (in angstroms; needs a decimal point).

  • wireframe 0.3

spacefill or cpk

Sets the diameter of the sphere representing an atom (most usually in percent, relative to Van der Waals radius)

  • spacefill
  • spacefill off
  • spacefill 30%


A schematic rendering that is relevant only to protein and nucleic acid chains.

  • cartoon
  • cartoon off
  • cartoon only


Same considerations.


Same considerations.

  • trace
  • trace off
  • trace only
  • trace 0.8
  • trace -0.5

display and hide

Reversibly removes part of the molecule from view (without changing the assigned rendering style). Note that its action is not cumulative, but exclusive.

  • display all ; back to normal state
  • display ligands ; and hide everything else
  • hide not ligands ; does the same
  • display [ATG]; display add _Mg ; cumulative action