Single-word Selectors: Difference between revisions

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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.
 
<TABLE BORDER="1">
<TR><TH ALIGN="CENTER">Single Word Selector</TH>
<TH ALIGN="CENTER">Short Form Selector</TH>
<TH ALIGN="CENTER">Description</TH></TR>
<TR><TD ALIGN="CENTER">all</TD><TD ALIGN="CENTER">*</TD><TD>All atoms currently loaded into PyMOL</TD></TR>
<TR><TD ALIGN="CENTER">none</TD><TD ALIGN="CENTER">none</TD>
<TD>No atoms (empty selection)</TD></TR>
<TR><TD ALIGN="CENTER">hydro</TD><TD ALIGN="CENTER">h.</TD>
<TD>All hydrogen atoms currently loaded into PyMOL</TD></TR>
<TR><TD ALIGN="CENTER">hetatm</TD><TD ALIGN="CENTER">het</TD>
<TD>All atoms loaded from Protein Data Bank HETATM records</TD></TR>
<TR><TD ALIGN="CENTER">visible</TD><TD ALIGN="CENTER">v.</TD>
<TD>All atoms in enabled objects with at least one visible representation</TD></TR>
<TR><TD ALIGN="CENTER">polymer</TD><TD ALIGN="CENTER"></TD>
<TD>All atoms on the polymer (not het).</TD></TR>
<TR><TD ALIGN="CENTER">present</TD><TD ALIGN="CENTER">pr.</TD><TD>All atoms with defined coordinates in the current state (used in creating movies)</TD></TR>
</TABLE>


{| 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>
== 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.