File: add_hydrogens.html

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
   
  <link href="documentation.css" rel="stylesheet" type="text/css">
  <title>Ghemical User Documentation - Add Hydrogens Tool</title>
</head>
  <body>
   
<h1>2.1.3 Add Hydogens Tool</h1>
   
<p>Instead of individually adding hydrogens to your molecule you may use the
Add Hydrogens  tool to add hydrogens to all open valences. After you've added
all the non-hydrogen atoms to your molecule, right click on the display and
select Build from the popup menu. Select Hydrogens from this menu and then
pick Add.</p>
  <img src="images/add_hydrogens_select.png" width="554" height="603"
 alt="Screenshot of add hydrogens selection.">
   
<p>Ghemical will then automatically add hydrogens to your molecule. Ghemical 
makes a simple attempt to position the hydrogens at their most stable orientation 
(tetrahedral in the case of carbon) however the molecule should still be optimized
to get a more accurate geometry.</p>
  <img src="images/add_hydrogens.png" width="554" height="603"
 alt="Screenshot of the add hydrogens tool.">
   
<h2>Remove Hydrogens</h2>
   
<p>Ghemical also provides a tool to remove all hydrogen atoms from the molecule. 
It is activated by right clicking on the view, selecting Build from the menu, 
selecting Hydrogens from the submenu and then selecting Remove</p>
  <img src="images/remove_hydrogens.png" width="556" height="602"
 alt="Screenshot of the remove hydrogens tool">
   
<hr> <br>
  <a href="index.html">Return to index.</a> <br>
</body>
</html>