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) |