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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><a name="_MailEndCompose"><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Elaine,<o:p></o:p></span></b></a></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks. Your suggestions were indeed very helpful. <br><br><o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I have another question that maybe you can answer. Is there a way in Chimera to select only internal amino acids of a protein (I would like to select hydrophobic amino acids away under the surface of my protein to try and identify hydrophobic core groups)?<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks!<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>John<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><div><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>John M. Beale, Jr., Ph.D.<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Professor of Medicinal Chemistry and Pharmacognosy<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Saint Louis College of Pharmacy<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>4588 Parkview Place<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Saint Louis, Missouri 63110<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>314-446-8461<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Cell: 314-315-0409<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>FAX: 314-446-8460</span></b><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#8064A2'><o:p></o:p></span></b></p><p class=MsoNormal><a href="mailto:jbeale@stlcop.edu"><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:blue'>jbeale@stlcop.edu</span></b></a><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></b></p></div><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></b></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='margin-left:.5in'><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Elaine Meng [mailto:meng@cgl.ucsf.edu] <br><b>Sent:</b> Monday, November 29, 2010 6:19 PM<br><b>To:</b> Beale, John<br><b>Cc:</b> chimera-users@cgl.ucsf.edu<br><b>Subject:</b> Re: [Chimera-users] Closest Waters<o:p></o:p></span></p></div></div><p class=MsoNormal style='margin-left:.5in'><o:p> </o:p></p><p class=MsoNormal style='margin-left:.5in'>Hi John,<o:p></o:p></p><div><p class=MsoNormal style='margin-left:.5in'>Please see the previous reply to a similar question:<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'><<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005459.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005459.html</a>><o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'>To summarize, the "Find Clashes/Contacts" tool identifies contacts of all types and "FindHBond" identifies hydrogen bonds. There are various choices of what to do with the identified contacts, such as selecting them or writing out all the information to a file. Selections can be further acted upon (for example, their residue labels shown) using the Actions menu. See the previous reply for links to the relevant manual pages. <o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'>Examples of use are included in the "Structure Analysis and Comparison" tutorial:<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html</a>><o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'><o:p> </o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'>Best,<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'>Elaine<o:p></o:p></p><div><div><div><div><p class=MsoNormal style='margin-left:.5in'>----------<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'>Elaine C. Meng, Ph.D. <o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'>Department of Pharmaceutical Chemistry<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'>University of California, San Francisco<o:p></o:p></p></div><div><p class=MsoNormal style='margin-left:.5in'><o:p> </o:p></p></div></div></div><div><div><p class=MsoNormal style='margin-left:.5in'>On Nov 29, 2010, at 12:10 PM, Beale, John wrote:<o:p></o:p></p></div><p class=MsoNormal style='margin-left:.5in'><br><br><o:p></o:p></p><div><div><p class=MsoNormal style='margin-left:.5in'><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#7030A0'>I am working with a protein in explicit water. Using AMBER tools, I have selected the 100 closest water molecules in and around the protein. Is there a way in Chimera to identify which amino acid residues that the waters are hydrogen bonded to? Or, is there a way to visualize which amino acids the water molecules are closest to?</span><o:p></o:p></p></div></div></div><p class=MsoNormal style='margin-left:.5in'><o:p> </o:p></p></div></div></div></body></html>