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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.5pt;font-family:"Verdana","sans-serif";color:black'>Hi Afshan,<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.5pt;font-family:"Verdana","sans-serif";color:black'>This is from the documentation online. <o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.5pt;font-family:"Verdana","sans-serif";color:black'><a href="http://www.phenix-online.org/documentation/refinement.htm">http://www.phenix-online.org/documentation/refinement.htm</a><o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.5pt;font-family:"Verdana","sans-serif";color:black'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.5pt;font-family:"Verdana","sans-serif";color:black'>7.To remove hydrogens from a model:<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>% phenix.pdbtools model.pdb remove=&quot;element H or element D&quot;<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in'><a name=anch205></a><span style='font-size:10.5pt;font-family:"Verdana","sans-serif";color:black'>or Reduce programs can be used for this:<o:p></o:p></span></p><p class=MsoNormal style='margin-left:.5in'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>% phenix.reduce model_h.pdb -trim &gt; model_noH.pdb<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in'><a name=anch206></a><span style='font-size:10.5pt;font-family:"Verdana","sans-serif";color:black'>We strongly recommend to not remove hydrogen atoms after refinement since it will make the refinement statistics (R-factors, etc...) unreproducible without repeating exactly the same refinement protocol.<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in'><span style='font-size:10.5pt;font-family:"Verdana","sans-serif";color:black'><o:p>&nbsp;</o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:.5in'><span style='font-size:10.5pt;font-family:"Verdana","sans-serif";color:black'>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>&nbsp;</o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p>&nbsp;</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"'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] <b>On Behalf Of </b>Afshan Begum<br><b>Sent:</b> Thursday, February 06, 2014 9:12 AM<br><b>To:</b> phenixbb@phenix-online.org<br><b>Subject:</b> [phenixbb] how to remove hydrogen from pdb<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p>&nbsp;</o:p></p><div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p>&nbsp;</o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'>&nbsp;Dear Experts,<br><br>Could you kindly tell me how can i remove hydrogen from my coordinate. Actually i refine my structure with phenix along all hydrogen now its almost done but before submitting the molecule into PDB data bank i want to remove hydrogen from the coordinate which i do not know how to do,&nbsp; suggestion would be appreciated</span><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#40007F'><br></span><b><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><br><br>Best Regards</span></b><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#40007F'><br></span><b><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><br>AFSHAN</span></b><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:#40007F'>===========================================<br><b>Dr. Afshan Begum&nbsp;</b></span><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black'><o:p>&nbsp;</o:p></span></p></div></div></div></body></html>