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Hi Jianghai,<br>
could you please tell which command you are running? I need to have
some more context to see where the problem comes from. Also it would be
helpful if you could briefly explain what you are trying to refine.
Does you model have H atoms?<br>
<br>
Thank you,<br>
Pavel.<br>
<br>
Jianghai Zhu wrote:
<blockquote
cite="mid684EE799-1A87-41BD-9C6C-C358A9D7663E@cbr.med.harvard.edu"
type="cite">Hi,
<div><br class="khtml-block-placeholder">
</div>
<div>In my refinement phenix.refine crashed with the following errors.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>================================ xyz refinement
===============================</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Traceback (most recent call last):</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/refine.py",
line 5, in <module></div>
<div> command_line.run(command_name="phenix.refine",
args=sys.argv[1:])</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/command_line.py",
line 78, in run</div>
<div>
call_back_after_monitor_collect=call_back_after_monitor_collect)</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py",
line 1310, in run</div>
<div> log = log)</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py",
line 733, in refinement_machine</div>
<div> h_params = h_params)</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/minimization.py",
line 136, in __init__</div>
<div> ignore_line_search_failed_step_at_lower_bound = True))</div>
<div> File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py",
line 242, in run</div>
<div> log)</div>
<div> File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py",
line 121, in run_c_plus_plus</div>
<div> f, g = target_evaluator.compute_functional_and_gradients()</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/minimization.py",
line 369, in compute_functional_and_gradients</div>
<div> u_iso_refinable_params = u_iso_refinable_params)</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/minimization.py",
line 224, in compute_target</div>
<div> sf_v3d_sel = sf_v3d.set_selected(self.hd_selection, [0,0,0])</div>
<div>RuntimeError: scitbx Internal Error:
/net/sharptail/scratch1/rwgk/auto_build/sources/scitbx/include/scitbx/array_family/boost_python/flex_wrapper.h(473):
SCITBX_ASSERT(a.accessor() == flags.accessor()) failure.</div>
<div><br class="khtml-block-placeholder">
</div>
<div><br class="khtml-block-placeholder">
</div>
<div>What happened here? Thanks.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Jianghai</div>
<div><br>
<div> <span class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;">
<div>+++++++++++++++++++++++++++++++</div>
<div>Jianghai Zhu, Ph.D</div>
<div>CBR Institute for Biomedical Research</div>
<div>Department of Pathology</div>
<div>Harvard Medical School</div>
<div>200 Longwood Ave., Boston, MA 02115</div>
<div>Ph: 617-278-3211</div>
<div>Fx: 618-278-3232</div>
<div>+++++++++++++++++++++++++++++++</div>
<div><br class="khtml-block-placeholder">
</div>
<br class="Apple-interchange-newline">
</span></span></span></span></span></span></span> </div>
<br>
</div>
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