Single-word Selectors

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).
present	pr.	All atoms with defined coordinates in the current state (used in creating movies)

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)