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</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=EN-US link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>A lot of the monomers are available in Coot and there are a couple different ways to access them for either integrating into a structure or generating a monomer pdb file to do some further minimizations and cif generation using elbow.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>In Coot - To change a residue in a protein structure, select the residue of interest and then ‘Extensions’ -> ‘Modeling’ -> ‘Replace residue’ . In the window that pops up type OCS. This will automatically change whatever residue you selected to OCS. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>To see/generate just the residue go to ‘File’ -> ‘Search Monomer Library’ and enter CYSTEINESULFONIC ACID. This should return the OCS monomer. You can then save that monomer as a pdb and generate a cif using elbow if the cif file isn’t already part of the phenix library. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hope that helps.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Ryan<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>--<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Ryan K. Spencer, Ph.D.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Postdoctoral Researcher<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hochbaum Laboratory<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Chemical Engineering & Material Sciences<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>University of California, Irvine<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext'> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] <b>On Behalf Of </b>Pavel Afonine<br><b>Sent:</b> Wednesday, March 30, 2016 1:30 AM<br><b>To:</b> Shilpa Janarthanan <shilpa.janarthanan@gmail.com>; phenixbb@phenix-online.org<br><b>Subject:</b> Re: [phenixbb] Selenocysteine<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi,<br><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><p class=MsoNormal><span style='font-family:"Georgia",serif'>How to add an unnatural amino acid (say OCS) at a position in the sequence and view it in PyMol, provided the protein structure (PDB file) is given? Is it correct to make changes in the PDB file itself, if Yes, then how should I do it?<o:p></o:p></span></p></div></div></blockquote><p class=MsoNormal style='margin-bottom:12.0pt'><br>at the risk of setting a bad example... If I had to do it myself I would edit PDB file manually to mutate existing residue into OCS, then I would run a quick geometry minimization to fix up geometry (that is likely to be distorted due to manual editing). If OCS is this <br><br>elbow.where_is_that_cif_file OCS<br><br>then everything may just work fine. Otherwise you may want to provide a CIF file for it.<br><br>I wonder if this kind of manipulation can be done in Coot?<br><br>Pavel<o:p></o:p></p></div></body></html>