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<p class="MsoNormal"><span style="font-size:12.0pt">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt">I am trying to do a phenix.real_space_refine in a CryoEM map at 4.2 Å with a model obtained by MDFF (NAMD, a protein DNA complex) because the resulting structure, despite a good CC and a good
molecular geometry has a poor Ramachandran Map.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt">When doing the phenix.real_space_refine, the CC is slightly increased with respect to the starting structure, the Ramachandran is dramatically increased but some part of the model ( in the case,
the first three bases pairs a DNA duplex) are strongly distorted because of a lack of density in the corresponding region of the map.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt">For some reason, this does not append with the MDFF method.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt">I was wondering if there is a mean, in phenix.real_space_refine, to exclude a part of the model from being fitted in the map. Indeed, the distortion I observe in the DNA duplex is likely due to
the fact that the real_space_refine tries to put the atoms at the extremity of the duplex in the closest density at the price of a strong distortion of the structure.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt">Thank in advance for your suggestions.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt">Best regards.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt">Philippe.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">-----------------------------------------------</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Philippe Cuniasse, PhD/HDR.</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Institut de Biologie Integrative de la cellule.</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">UMR 9198 CNRS-CEA-Univ Paris Sud</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Bat 144 CE-Saclay</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">91191 Gif-sur-Yvette Cedex</span><span style="font-size:13.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">France</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Tel: (33) 1 69 08 56 35</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Fax: (33) 1 69 08 47 12</span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Email: </span><span style="font-size:9.0pt;font-family:Courier;color:#0000FE;mso-fareast-language:FR"><a href="mailto:philippe.cuniasse@cea.fr"><span style="color:purple">philippe.cuniasse@cea.fr</span></a></span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">Web:</span><span style="font-size:9.0pt;font-family:Courier;color:#0000F5;mso-fareast-language:FR"> <a href="http://biodev.cea.fr/rasmot3d/"><span style="color:purple">http://biodev.cea.fr/rasmot3d/</span></a></span><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;color:black;mso-fareast-language:FR"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><i><span style="font-size:10.0pt;font-family:"Times New Roman",serif;color:black;mso-fareast-language:FR"><img border="0" id="Image_x0020_3" src="cid:image001.png@01D98746.BF92A6E0" alt="signature_3454313285"></span></i></b><span style="font-size:12.0pt;font-family:"Comic Sans MS";color:black;mso-fareast-language:FR"><img border="0" id="Image_x0020_2" src="cid:image002.png@01D98746.BF92A6E0" alt="signature_3433042689"><img border="0" id="Image_x0020_1" src="cid:image003.png@01D98746.BF92A6E0" alt="signature_3416814468"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Courier;color:black;mso-fareast-language:FR">-----------------------------------------------</span><span style="font-size:14.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:14.0pt"><o:p> </o:p></span></p>
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