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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Helena,<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">from the symptoms you are describing I am guessing that your definition of alternate conformations is somehow not correct. How did you generate the alternate
conformations, in COOT, by hand, or by some other means? In my hands I only see the problem of bumping residues out of density when the alternate conformations are ill defined. <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">This example (not tested) should work. The alternate location indicator is in column 17 (http://www.ccp4.ac.uk/html/pdbformat.html)<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:"Courier New";color:#1F497D">1 10 20 30 40 50 60 70 80<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">|........|.........|.........|.........|.........|.........|.........|.........|<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2133 N AARG B 5 -8.859 76.908 -23.554 0.50 62.53 N<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2134 CA AARG B 5 -7.595 77.592 -23.916 0.50 73.84 C<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2135 CB AARG B 5 -6.685 77.736 -22.691 0.50 68.34 C<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2136 CG AARG B 5 -7.156 78.775 -21.687 0.50 64.25 C<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2137 CD AARG B 5 -6.073 79.165 -20.698 0.00 65.04 C<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2138 NE AARG B 5 -6.494 80.270 -19.841 0.00 63.73 N<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2139 CZ AARG B 5 -5.692 80.907 -18.995 0.00 62.76 C<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2140 NH1AARG B 5 -4.419 80.552 -18.890 0.00 62.59 N<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2141 NH2AARG B 5 -6.161 81.902 -18.255 0.00 62.33 N<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2142 C AARG B 5 -6.823 76.908 -25.061 0.50 90.43 C<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2143 O AARG B 5 -6.316 77.579 -25.965 0.50 84.57 O<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2144 N BARG B 5 -8.759 76.908 -23.554 0.50 62.53 N<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2145 CA BARG B 5 -7.495 77.592 -23.916 0.50 73.84 C<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2146 CB BARG B 5 -6.585 77.736 -22.691 0.50 68.34 C<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2147 CG BARG B 5 -7.124 78.675 -21.625 0.50 64.25 C<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2148 CD BARG B 5 -6.176 78.831 -20.450 0.50 65.04 C<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2149 NE BARG B 5 -6.742 79.680 -19.405 0.50 63.73 N<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2150 CZ BARG B 5 -6.175 79.889 -18.223 0.50 62.76 C<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2151 NH1BARG B 5 -5.018 79.312 -17.929 0.50 62.59 N<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2152 NH2BARG B 5 -6.761 80.679 -17.334 0.50 62.33 N<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2153 C BARG B 5 -6.723 76.908 -25.061 0.50 90.43 C<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">ATOM 2154 O BARG B 5 -6.216 77.579 -25.965 0.50 84.57 O<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">HTH
<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">Carsten<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>
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<p class="MsoNormal"><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""> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org]
<b>On Behalf Of </b>Helena Taberman<br>
<b>Sent:</b> Monday, January 11, 2016 6:55 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] Additional conformations and partially occupied waters<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I’m trying to refine a structure determined to 1.6 Å resolution. There’s several residues with additional conformations and waters with partial occupancies stating that they would be there when the conformation of the residues allows it.
When I try to refine these conformations and partially occupied waters together the refinement kicks the second conformations and water molecules out of their densities, since they are obviously too close to the other additional conformations of the residues
or the following residues. What could I do? Should I somehow group them together or what?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best regards,<o:p></o:p></p>
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<p class="MsoNormal">Helena<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:black">Helena Taberman, Ph.D.<br>
<br>
University of Eastern Finland<br>
Department of Chemistry<br>
Joensuu Campus<br>
P.O. Box 111<br>
FI-80101 Joensuu, FINLAND<br>
<br>
Mobile: +358 50 337 2488<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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