Difference between revisions of "Single-word Selectors"
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Jaredsampson (talk | contribs) (added list of selectors (from Selector.c in source), excluding deprecated forms) |
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== 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. | + | 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. |
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+ | {| class="wikitable" | ||
+ | |- | ||
+ | ! 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. | The selector '''none''' won't come up much when you are typing commands directly into PyMOL, but it is useful in programming scripts. | ||
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# are represented as spheres. | # are represented as spheres. | ||
</pre> | </pre> | ||
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+ | == More selectors == | ||
+ | {| class="wikitable" | ||
+ | |- | ||
+ | ! 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. | ||
+ | | | ||
+ | |- | ||
+ | | restrained | ||
+ | | rst. | ||
+ | | | ||
+ | |- | ||
+ | | organic | ||
+ | | org. | ||
+ | | | ||
+ | |- | ||
+ | | inorganic | ||
+ | | ino. | ||
+ | | | ||
+ | |- | ||
+ | | solvent | ||
+ | | sol. | ||
+ | | All water molecules. | ||
+ | |} | ||
Revision as of 11:26, 5 December 2011
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. | |
restrained | rst. | |
organic | org. | |
inorganic | ino. | |
solvent | sol. | All water molecules. |