Single-word Selectors: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
Jaredsampson (talk | contribs) (added list of selectors (from Selector.c in source), excluding deprecated forms) |
||
Line 1: | Line 1: | ||
== 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. | ||
{| 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. | ||
Line 37: | Line 53: | ||
# are represented as spheres. | # are represented as spheres. | ||
</pre> | </pre> | ||
== 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. |