Single-word Selectors - Revision history

Cchem: 1 revision

2017-12-11T04:50:19Z

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Speleo3: redirect Selection Algebra

2017-11-21T11:55:55Z

redirect Selection Algebra

Cchem: 1 revision

2016-05-01T04:43:42Z

1 revision

Speleo3: center, origin

2016-04-20T13:45:52Z

center, origin

Bell: 14 revisions

2014-03-28T03:36:08Z

14 revisions

Speleo3: backbone/sidechain

2013-09-08T11:53:41Z

backbone/sidechain

Speleo3: metals

2013-08-13T16:01:49Z

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Speleo3: guide

2012-03-05T13:28:34Z

guide

New page

== 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.

{| 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.

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.
</source>

== 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.
| 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'
|}

[[Category:Selector Quick Reference]]

[[Category:Selecting|Single Word Selectors]]
[[Category:States]]

Jaredsampson: /* More selectors */

2011-12-05T15:29:49Z

More selectors

Jaredsampson: /* More selectors */ added a couple more descriptions to the list

2011-12-05T15:29:17Z

More selectors: added a couple more descriptions to the list

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	== Single-word Selectors ==		== Single-word Selectors ==

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← Older revision	Revision as of 04:43, 1 May 2016
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 | pr.
 | All atoms with defined coordinates in the current state (used in creating movies)
 |}

← Older revision	Revision as of 03:36, 28 March 2014
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@@ Line 32: / Line 32: @@
 | pol.
 | All atoms on the polymer (not het).
 |-
 | present

@@ Line 108: / Line 108: @@
+|
 | All protein CA and nucleic acid C4*/C4'
 |}

@@ Line 88: / Line 88: @@
 | fixed
 | fxd.
+| All fixed atoms.
 |-
 | restrained
 | rst.
+| All restrained atoms.
 |-
 | organic

@@ Line 96: / Line 96: @@
 | organic
 | org.
+| All atoms in non-polymer organic compounds (e.g. ligands, buffers).
 |-
 | inorganic
 | ino.
+| All non-polymer inorganic atoms/ions.
 |-
 | solvent