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| + | #REDIRECT [[Selection Algebra]] | ||
| + | |||
== Single-word Selectors == | == Single-word Selectors == | ||
| Line 32: | Line 34: | ||
| pol. | | pol. | ||
| All atoms on the polymer (not het). | | 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 | | present | ||
| pr. | | pr. | ||
| All atoms with defined coordinates in the current state (used in creating movies) | | 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 | ||
|} | |} | ||
| Line 42: | Line 60: | ||
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. | 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. | ||
| − | < | + | <source lang="python"> |
| − | + | 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. | # are represented as spheres. | ||
| − | </ | + | </source> |
| − | |||
== More selectors == | == More selectors == | ||
| Line 105: | Line 122: | ||
| sol. | | sol. | ||
| All water molecules. | | All water molecules. | ||
| + | |- | ||
| + | | guide | ||
| + | | | ||
| + | | All protein CA and nucleic acid C4*/C4' | ||
| + | |- | ||
| + | | metals | ||
| + | | | ||
| + | | All metal atoms ''(new in PyMOL 1.6.1)'' | ||
|} | |} | ||
Latest revision as of 04:50, 11 December 2017
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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) |