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<title>Ghemical User Documentation: Sequence Builder</title>
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<h1>2.1.13 Sequence Builder</h1>
<p>Ghemical has a tool to simplify building amino and nucleic acid sequences.
The Sequencer Builder allows the user to enter a string of letters denoting
amino or nucleic acid sequences. To activate the sequence builder, right
click on the view, select Build from the pop-up menu and then select either Sequence
Builder (amino) or Sequence Builder (nucleic).</p>
<img src="images/aa_builder_menu.png" width="401" height="315" alt="Screenshot of the sequence buider menu.">
<p>This tool currently reads it's input from a textbox. You will need to change the
text "AAA" to the amino acid sequence of the peptide you are building. A window
containing explaining this will appear after you click on the sequence builder.
</p>
<img src="images/aa_builder_note.png" width="525" height="179" alt="Screenshot of the information box explaining the Sequence Builder tool.">
<p>
The sequence should be entered as a string of the one letter abbreviations for
the acids without spaces or other punctuation. When you are done entering
the sequence, click Ok.</p>
<img src="images/aa_builder_ci.png" width="411" height="98" alt="Screenshot of the sequence builder command interpreter textbox.">
<p>The chain will appear in the view window, and you may manipulate it in
the same way as you would any other molecule. The sequences are built without
hydrogens, so if you want to have the hydrogens present you must add them
with the Add Hydrogen tool. </p>
<img src="images/aa_builder_wo_h.png" width="498" height="633" alt="Screenshot of a polypeptide built by the sequence builder.">
<p>For convinience, a table of amino acids and their abbreviations is reproduced
<a href="aa_table.html">here</a>.</p>
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