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<h1 class="page-title">Tutorial: Selection Language</h1>
<section>
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<h2>Selection Language</h2>
</header>
<article>
<h1>Selection Language</h1>
<p>Miew allows to view different molecule parts (subsets of atoms) using specific visualizations.
To select these subsets one should use a <em>Selection Language</em>; find the description of its syntax below.</p>
<h2>Quick Examples</h2>
<ul>
<li><code>chain A and not hetatm</code><br>
select all atoms in chain A except for HETATM PDB records.</li>
<li><code>residue ALA</code><br>
select all residues named <code>ALA</code> (alanine).</li>
<li><code>serial 1:10, 20:30 and type C, N</code><br>
select Carbon and Nitrogen atoms with atom indices in range 1 through 10 or
20 through 30 inclusively.</li>
</ul>
<h2>Syntax</h2>
<p>An <em>Expression</em> in Miew selection language consists of a <em>Selector</em> or a set of <em>Expressions</em>
joined with logical operations <code>AND</code>, <code>OR</code>, <code>NOT</code> and brackets for grouping.</p>
<pre><code>Expression ::=
Selector |
Expression 'AND' Expression |
Expression 'OR' Expression |
'NOT' Expression |
'(' Expression ')'
</code></pre>
<p><em>Selector</em> consists of a keyword followed by an optional comma separated parameter list.
Some keywords accept integer parameters (e.g. atom or residue indices), others accept strings
(e.g. atom or residue names). Keywords are <strong>case insensitive</strong>.</p>
<p>Integer parameter can be a single value or range of values, where colon delimits range borders.
Example: <code>3:7</code> defines an integer range: 3, 4, 5, 6, and 7).</p>
<p>There should be quotation marks for string parameters unless the string consists of letters,
digits and underscores only.</p>
<pre><code>Selector ::=
Keyword |
Keyword IntegerList |
Keyword StringList
IntegerList ::= Range | IntegerList ',' Range
Range ::= Number | Number ':' Number
StringList ::= String | StringList ',' String
String ::= AlphaNumericString | QuotedString
</code></pre>
<h2>Keywords list</h2>
<table>
<thead>
<tr>
<th>Keyword</th>
<th>Description</th>
<th>Example</th>
</tr>
</thead>
<tbody>
<tr>
<td><strong>all</strong></td>
<td>all atoms</td>
<td>all</td>
</tr>
<tr>
<td><strong>none</strong></td>
<td>empty subset</td>
<td>none</td>
</tr>
<tr>
<td><strong>hetatm</strong></td>
<td>atoms defined as HETATM in PDB-file</td>
<td>not hetatm</td>
</tr>
<tr>
<td><strong>water</strong></td>
<td>water residues (WAT, HOH, H2O)</td>
<td>hetatm and not water</td>
</tr>
<tr>
<td><strong>serial</strong> <em>int</em></td>
<td>atoms by serial numbers</td>
<td>serial 1:10, 13, 25:37</td>
</tr>
<tr>
<td><strong>name</strong> <em>str</em></td>
<td>atoms by names</td>
<td>name CA, CB</td>
</tr>
<tr>
<td><strong>elem</strong> <em>str</em></td>
<td>atoms by chemical elements</td>
<td>elem O, N, H</td>
</tr>
<tr>
<td><strong>type</strong> <em>str</em></td>
<td><em>deprecated!</em> superseded by <strong>elem</strong></td>
<td></td>
</tr>
<tr>
<td><strong>altloc</strong> <em>str</em></td>
<td>atoms by alternative location (conformation)</td>
<td>altloc " ", A</td>
</tr>
<tr>
<td><strong>residue</strong> <em>str</em></td>
<td>residues by names</td>
<td>residue ALA, CYS</td>
</tr>
<tr>
<td><strong>sequence</strong> <em>int</em></td>
<td>residues by indices in a sequence</td>
<td>sequence 35:37</td>
</tr>
<tr>
<td><strong>residx</strong> <em>int</em></td>
<td>residues by ordinal index</td>
<td>residx 1327</td>
</tr>
<tr>
<td><strong>icode</strong> <em>str</em></td>
<td>residues by insertion code</td>
<td>sequence 409 and icode B</td>
</tr>
<tr>
<td><strong>protein</strong></td>
<td>one of 22 common amino acid residues</td>
<td></td>
</tr>
<tr>
<td><strong>basic</strong></td>
<td>basic amino acid residue: ARG, HIS, LYS</td>
<td></td>
</tr>
<tr>
<td><strong>acidic</strong></td>
<td>acidic amino acid residue: ASP, GLU</td>
<td></td>
</tr>
<tr>
<td><strong>charged</strong></td>
<td>basic or acidic residue</td>
<td></td>
</tr>
<tr>
<td><strong>polar</strong></td>
<td>polar amino acid residue: ASN, CYS, GLN, SER, THR, TYR</td>
<td></td>
</tr>
<tr>
<td><strong>nonpolar</strong></td>
<td>non-polar amino acid residue: ALA, ILE, LEU, MET, PHE, PRO, TRP, VAL</td>
<td></td>
</tr>
<tr>
<td><strong>aromatic</strong></td>
<td>aromatic amino acid residue: PHE, TRP, TYR</td>
<td></td>
</tr>
<tr>
<td><strong>nucleic</strong></td>
<td>nucleic residue</td>
<td></td>
</tr>
<tr>
<td><strong>purine</strong></td>
<td>purine nucleic residue: A, G, I and variations</td>
<td></td>
</tr>
<tr>
<td><strong>pyrimidine</strong></td>
<td>pyrimidine nucleic residue: C, T, U and variations</td>
<td></td>
</tr>
<tr>
<td><strong>polarh</strong></td>
<td>polar hydrogens are hydrogens that are boud to anything other than carbon, e.g. nitrogen, oxygen, sulphur</td>
<td></td>
</tr>
<tr>
<td><strong>nonpolarh</strong></td>
<td>non-polar hydrogens are hydrogens that are bonded to carbon</td>
<td></td>
</tr>
<tr>
<td><strong>chain</strong> <em>str</em></td>
<td>chain by name</td>
<td>chain A, C, E</td>
</tr>
</tbody>
</table>
</article>
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