That&#39;s a good question...<br>In a first approximation you could assume that all atoms not classified as acceptors/donors of protons would be hydrophobic. This is essentially carbons. If you represent the surface of the molecule colored by elements you should see these pockets.<br>

<br>More sophisticated approaches include the program GRID (<a href="http://www.moldiscovery.com/soft_grid.php" target="_blank">http://www.moldiscovery.com/soft_grid.php</a>) to compute the hydrophobic potential (Goodford, P.J., A computational procedure for determining
energetically favourable binding sites on biologically important
macromolecules. <i>J. Med. Chem. </i><b>28</b>, 849-57.)<br><br>Unfortunately, GRID is not free, not even for academics (though there is a special price for the license). Anyway, I think it would be nice if chimera could map the hydrophobic potential maps onto molecular surfaces.<br>
<br>Best,<br><br><br>Miguel<br><br><div class="gmail_quote">2008/6/27 bala &lt;<a href="mailto:bala@igib.res.in" target="_blank">bala@igib.res.in</a>&gt;:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">

<div><div><font color="#000000" face="Arial" size="2">Dear Chimerian&#39;s,</font></div>
<div><font face="Arial" size="2"></font>&nbsp;</div>
<div><font face="Arial" size="2">How do i&nbsp;detect hydrophobic pockets in a 
protein using chimera ?. </font></div>
<div><font face="Arial" size="2"></font>&nbsp;</div>
<div><font face="Arial" size="2">Thanks in advance,</font></div>
<div><font face="Arial" size="2">Bala</font></div></div><br>_______________________________________________<br>
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<br></blockquote></div><br><br clear="all"><br>-- <br><a href="http://www.pangea.org/mol/spip.php?rubrique2" target="_blank">http://www.pangea.org/mol/spip.php?rubrique2</a><br>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<br>

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