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    <div class="moz-cite-prefix">Hi Subhani,<br>
      <br>
      please send me the inputs off list and I will check what's
      happening with R-factors.<br>
      <br>
      Thanks,<br>
      Pavel<br>
      <br>
      On 7/1/13 1:09 PM, Subhani Bandara wrote:<br>
    </div>
    <blockquote
cite="mid:CAPCm4u8X8u=3f4z4ZAJ1kGZgxuONyjHprTX3XHL85dvy33CNqA@mail.gmail.com"
      type="cite">
      <div dir="ltr">Dear all,
        <div><br>
        </div>
        <div>I am refining a protein structure at 2.5 A.&nbsp;</div>
        <div><br>
        </div>
        <div>After running some refinements with water update option on,
          I manually added water to some positions and ran without water
          update option as it removes those water from the sites and
          show green density around. &nbsp; &nbsp;Then after some refinements like
          this, I tried to use water update option to add water to some
          newly appeared density. &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
          &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</div>
        <div><br>
        </div>
        <div>When I check the option to update water using dev 1418
          version it stops with the following error. &nbsp;Also &nbsp;when not
          using water update option, refinement statistics got worse
          when I used 1418 compared to&nbsp;1.8.2-1309&nbsp;with refinements using
          same inputs and options.</div>
        <div><br>
        </div>
        <div style="">R work-0.1988 compared to 0.1920 with&nbsp;1.8.2-1309</div>
        <div style="">Rfree-0.2623 compared to 0.2490 with&nbsp;1.8.2-1309</div>
        <div>
          <p style="margin:0px;font-size:12px;font-family:Courier">Traceback:</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/thread_utils.py",
            line 236, in run</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            return_value = self._target(self._args, self._kwargs,
            self._c)</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py",
            line 94, in __call__</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            result = self.target()</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/cctbx_project/libtbx/runtime_utils.py",
            line 73, in __call__</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            result = self.run()</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py",
            line 69, in run</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            refine_object = self._run(args, callback)</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/runtime.py",
            line 85, in _run</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            call_back_handler=callback)</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/command_line.py",
            line 161, in run</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            call_back_handler=call_back_handler)</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/driver.py",
            line 1630, in run</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            ncs_manager &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = self.ncs_manager).result</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/strategies.py",
            line 155, in __init__</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            neutron_refinement2 = self.neutron_refinement2)</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py",
            line 26, in __init__</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            self.__call__()</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py",
            line 36, in __call__</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            self.__getattribute__(method_name)()</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py",
            line 106, in run_sol</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            mc &nbsp; = self.macro_cycle)</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp;
            File
            "/Applications/PHENIX-dev-1418/Contents/phenix-dev-1418/phenix/phenix/refinement/task_table.py",
            line 79, in _need_to_run</p>
          <p style="margin:0px;font-size:12px;font-family:Courier">&nbsp; &nbsp;
            else: raise RuntimeError("Not a valid mode: %s"%mode)</p>
          <p
            style="margin:0px;font-size:12px;font-family:Courier;min-height:14px"><br>
          </p>
          <p style="">Thanks in advance for any help</p>
          <p style="">Subhani</p>
          <p><br>
          </p>
        </div>
      </div>
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      <br>
      <pre wrap="">_______________________________________________
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