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<!--#set var="TITLE" value="Babel Plugin, Version 1.12"-->
<!--#include virtual="/Research/vmd/include/header-vmd.shtml"-->

<p>This plugin reads and displays molecular structure files in 
   several formats using the Babel program to translate them into
   PDB files which are easily read by VMD.  In order to use this plugin
   Babel 1.6 must be installed on your computer and must be executable 
   in your default command path so that the Babel plugin can run it 
   via calls to system().  Babel 1.6 is available from the
   <a href="http://www.eyesopen.com/products/applications/babel.html">OpenEye Babel web site</a>
</p>

<p>This table lists all of the molecule file formats that Babel will 
   translate to the PDB format which can be loaded by VMD:
</p>

<table>
<tr>
<td>Alchemy</td>
<td>AMBER PREP</td>
<td>Ball and Stick</td>

<tr>
<td>Biosym .CAR</td>
<td>Boogie</td> 
<td>Cacao Cartesian</td>

<tr>
<td>Cambridge CADPAC</td>
<td>CHARMm</td>
<td>Chem3D Cartesian 1</td>

<tr>
<td>Chem3D Cartesian 2</td>
<td>CSD CSSR</td>
<td>CSD FDAT</td>

<tr>
<td>CSD GSTAT</td>
<td>Free Form Fractional</td>
<td>GAMESS Output</td>

<tr>
<td>Gaussian Z-Matrix</td>
<td>Gaussian Output</td>
<td>Hyperchem HIN</td>

<tr>
<td>Mac Molecule</td>
<td>Macromodel</td>
<td>Micro World</td>

<tr>
<td>MM2 Input</td>
<td>MM2 Ouput</td>
<td>MM3</td>

<tr>
<td>MMADS</td>
<td>MDL MOLfile</td>
<td>MOLIN</td>

<tr>
<td>Mopac Cartesian</td>
<td>Mopac Internal</td>
<td>Mopac Output</td>

<tr>
<td></td>
<td>ShelX</td>
<td>Sybyl Mol</td>

<tr>
<td></td>
<td>Sybyl Mol2</td>
<td>XYZ</td>
</table>  

<h3>Notes:</h3>

<p><b>Read-only</b>
<br>This plugin is used only to read files. VMD does not currently support
    writing to these formats.</p>
</p>

<p><b>Unused data</b>
<br>Babel performs a reasonable translation in most cases, however 
    it is unavoidable that some formats may contain information which
    doesn't have a corresponding record in PDB files, so this information
    may be lost in the translation, and thus unavailble when loaded into VMD.
</p>

<p><b>Compressed files</b>
<br>Compressed files will need to be expanded before this plugin can read
them.
</p>

<!--#include virtual="/Research/vmd/include/footer-vmd.shtml"-->