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<div class="moz-cite-prefix">Engin,<br>
<br>
it's actually me.. I'm rewriting some parts of phenix.refine,
slowly, so some accidental glitches (that were not caught by our
test) are possible in nightly builds. Sorry.<br>
<br>
Pavel<br>
<br>
On 7/1/13 1:58 PM, Engin Özkan wrote:<br>
</div>
<blockquote cite="mid:51D1ED87.4010505@stanford.edu" type="cite">
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<div class="moz-cite-prefix">For the error you got with dev-1418,
I thought I would beat Nat to the punch, and tell you that the
ordered_solvent modes have recently changed. So, you just have
to go to All parameters -> Ordered solvent, and set the mode.<br>
<br>
Engin<br>
<br>
On 7/1/13 3:09 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. </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 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 style="">Thanks in advance for any help</p>
<p style="">Subhani</p>
<p><br>
</p>
</div>
</div>
<br>
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</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
w ph: (650)-498-7111
cell: (650)-862-8563</pre>
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