<div dir="ltr">Dear all,<div><br></div><div>I am refining a protein structure at 2.5 A. </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. Then after some refinements like this, I tried to use water update option to add water to some newly appeared density. </div>
<div><br></div><div>When I check the option to update water using dev 1418 version it stops with the following error. Also when not using water update option, refinement statistics got worse when I used 1418 compared to 1.8.2-1309 with refinements using same inputs and options.</div>
<div><br></div><div style>R work-0.1988 compared to 0.1920 with 1.8.2-1309</div><div style>Rfree-0.2623 compared to 0.2490 with 1.8.2-1309</div><div>
<p></p><p style="margin:0px;font-size:12px;font-family:Courier">Traceback:</p>
<p style="margin:0px;font-size:12px;font-family:Courier"> 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"> 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"> 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"> 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"> 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"> 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"> 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"> 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"> 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"> 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"> 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"> 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"> 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"> ncs_manager = 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"> 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"> 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"> 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"> 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"> 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"> 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"> 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"> mc = 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"> 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"> 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></p>
<p style>Thanks in advance for any help</p><p style>Subhani</p><p><br></p></div></div>