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Single-word Selectors

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Single-word Selectors

The very simplest selection-expressions are single-word selectors. These selectors do not take identifiers; they are complete by themselves. Below are some commonly used single-word selectors.

Single-Word Selector Short-Form Selector Description
all * All atoms currently loaded into PyMOL
none none No atoms (empty selection)
hydro h. All hydrogen atoms currently loaded into PyMOL
hetatm het All atoms loaded from Protein Data Bank HETATM records
visible v. All atoms in enabled objects with at least one visible representation
polymer pol. All atoms on the polymer (not het).
backbone bb. Polymer backbone atoms (new in PyMOL 1.6.1)
sidechain sc. Polymer non-backbone atoms (new in PyMOL 1.6.1)
present pr. All atoms with defined coordinates in the current state (used in creating movies)
center Pseudo-atom at the center of the scene
origin Pseudo-atom at the origin of rotation

The selector none won't come up much when you are typing commands directly into PyMOL, but it is useful in programming scripts.

As the table shows, many single-word selectors have short forms to save on typing. Some short forms must be followed by a period and a space, in order to delimit the word. Short forms and long forms have the same effect, so choose the form that suits you.

PyMOL> color blue, all          # It all turns blue.
PyMOL> color blue, *
PyMOL> hide hydro               # Representations of all 
PyMOL> hide h.                  # hydrogen atoms are hidden.
PyMOL> show spheres, hetatom    # All the atoms defined as HETATOMS 
PyMOL> show spheres, het        # in the PDB input file
                                   # are represented as spheres.

More selectors

Single-Word Selector Short-Form Selector Description
enabled All enabled objects or selections from the object list.
masked msk. All masked atoms.
protected pr. All protected atoms.
bonded All bonded atoms
donors don. All hydrogen bond donor atoms.
acceptors acc. All hydrogen bond acceptor atoms.
fixed fxd. All fixed atoms.
restrained rst. All restrained atoms.
organic org. All atoms in non-polymer organic compounds (e.g. ligands, buffers).
inorganic ino. All non-polymer inorganic atoms/ions.
solvent sol. All water molecules.
guide All protein CA and nucleic acid C4*/C4'
metals All metal atoms (new in PyMOL 1.6.1)