<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">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 &lt;module&gt;</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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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></BODY></HTML>