Editing Property Selectors (section)

==Property Selectors==
PyMOL reads data files written in PDB, MOL/SDF, Macromodel, ChemPy Model, and Tinker XYZ formats. Some of the data fields in these formats allow PyMOL to assign properties to atoms. You can group and select atoms according to these properties using property selectors and identifiers: the selectors correspond to the fields in the data files, and the identifiers correspond to the target words to match, or the target numbers to compare.

===General===
The items in a list of identifiers are separated by plus signs (+) only. Do not add spaces within a list of identifiers. The selector '''resi''' takes (+)-separated lists of identifiers, as in
<source lang="python">
PyMOL> select nterm, resi 1+2+3
</source>
or, alternatively, it may take a range given with a dash
<source lang="python">
PyMOL> select nterm, resi 1-3
</source>
The identifier for a blank field in an input file is an empty pair of quotes
<source lang="python">
PyMOL> select unstruct, ss ""   # A named selection is created
                                # to contain all atoms that are not assigned 
                                # a secondary structure.
</source>

===Property Selector Table===
Most property selectors select matches to their identifiers
<TABLE BORDER="1">
<TR><TH>Matching Property Selector</TH>
<TH ALIGN="CENTER"> Short Form Selector</TH>
<TH> Identifier and Example</TH>
</TR>
<TR><TD ALIGN="CENTER"> symbol</TD><TD ALIGN="CENTER"> e.</TD><TD><I>

chemical-symbol-list</I>
<BR> list of 1- or 2-letter chemical symbols from the periodic table
<BR>
<pre>PyMOL> select polar, symbol O+N</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">name</TD><TD ALIGN="CENTER"> n.</TD><TD><I>
atom-name-list</I>
<BR> list of up to 4-letter codes for atoms in proteins or nucleic acids
<BR>
<pre>PyMOL> select carbons, name CA+CB+CG+CD</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">resn</TD><TD ALIGN="CENTER"> r.</TD><TD><I>
residue-name-list</I>
<BR> list of 3-letter codes for amino acids
<BR>
<pre>PyMOL> select aas, resn ASP+GLU+ASN+GLN</pre>
or list of up to 2-letter codes for nucleic acids
<BR>
<pre>PyMOL&gt; select bases, resn A+G</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">resi</TD><TD ALIGN="CENTER"> i.</TD><TD><I>

residue-identifier-list</I>
<BR> list of up to 4-digit residue numbers
<BR>
<pre>PyMOL> select mults10, resi 1+10+100+1000</pre>
<I> residue-identifier-range</I>
<BR>
<pre>PyMOL&gt; select nterm, resi 1-10</pre>

</TD></TR>
<TR><TD ALIGN="CENTER">alt</TD><TD ALIGN="CENTER"> alt</TD><TD><I>
alternate-conformation-identifier-list</I>
<BR> list of single letters
<pre>PyMOL> select altconf, alt A+&quot;&quot;</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">chain</TD><TD ALIGN="CENTER"> c.</TD><TD><I>

chain-identifier-list</I>
<BR> list of single letters or sometimes numbers
<BR>
<pre>PyMOL> select firstch, chain A</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> segi</TD><TD ALIGN="CENTER"> s.</TD><TD><I>
segment-identifier-list</I>
<BR> list of up to 4 letter identifiers
<pre>PyMOL> select ligand, segi lig </pre>
</TD></TR>
<TR><TD ALIGN="CENTER">flag</TD><TD ALIGN="CENTER"> f.</TD><TD><I>
flag-number</I>
<BR> a single integer from 0 to 31
<BR>

<pre>PyMOL> select f1, flag 0</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">&nbsp; numeric_type &nbsp;</TD><TD ALIGN="CENTER"> nt.</TD><TD>
<I> type-number</I>
<BR> a single integer
<BR>
<pre>PyMOL> select type1, nt. 5</pre>

</TD></TR>
<TR><TD ALIGN="CENTER">text_type</TD><TD ALIGN="CENTER"> tt.</TD><TD><I>
type-string</I>
<BR> a list of up to 4 letter codes
<pre>PyMOL> select subset, text_type HA+HC</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">id</TD><TD ALIGN="CENTER"> id</TD><TD><I>

external-index-number</I>
<BR> a single integer
<BR>
<pre>PyMOL> select idno, id 23</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">index</TD><TD ALIGN="CENTER"> idx.</TD><TD><I>
internal-index-number</I>
<BR> a single integer
<BR>
<pre>PyMOL> select intid, index 11</pre>
</TD></TR>
<TR><TD ALIGN="CENTER"> ss</TD><TD ALIGN="CENTER"> ss</TD><TD><I>
secondary-structure-type</I>
<BR> list of single letters
<BR>
<pre>PyMOL> select allstrs, ss H+S+L+&quot;&quot;</pre>
</TD></TR>
</TABLE>



===Numeric Selector Table===
Other ''property selectors'' select by comparison to numeric identifiers

<TABLE BORDER="1">
<TR><TH>Numeric Selector</TH>
<TH ALIGN="CENTER"> Short Form</TH>
<TH>Argument and Example</TH></TR>
<TR><TD ALIGN="CENTER">b</TD><TD ALIGN="CENTER"> b</TD><TD><I>
comparison-operator b-factor-value</I>
<BR> a real number
<pre>PyMOL> select fuzzy, b &gt; 10</pre>

</TD></TR>
<TR><TD ALIGN="CENTER">q</TD><TD ALIGN="CENTER"> q</TD><TD><I>
comparison-operator occupancy-value</I>
<BR> a real number
<pre>PyMOL> select lowcharges, q &lt;0.50</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">&nbsp; formal_charge &nbsp;</TD><TD ALIGN="CENTER"> fc.</TD><TD>

<I> comparison-operator formal charge-value</I>
<BR> an integer
<pre>PyMOL> select doubles, fc. = -1</pre>
</TD></TR>
<TR><TD ALIGN="CENTER">&nbsp; partial_charge &nbsp;</TD><TD ALIGN="CENTER"> pc.</TD><TD>
<I> comparison-operator partial charge-value</I>
<BR> a real number
<pre>PyMOL> select hicharges, pc. &gt; 1</pre>
</TD></TR>
</TABLE>