id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2570 Some help files crash ChimeraX Tristan Croll Greg Couch "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core ChimeraX Version: 0.91 (2019-11-13) Description I'm getting an intermittent segmentation fault when clicking some command help links for Clipper and ISOLDE. Doesn't happen every time (1 in 2-3), and seemingly only when (a) the link goes to an anchor near the top of the page, and (b) the Help browser is closed before clicking the link. In the example shown in the log I can safely click any of the links other than ""clipper open"" with the Help browser closed, and with the browser already open I can safely click any of them. But if the browser is closed, clicking ""clipper open"" usually crashes ChimeraX with the traceback below. I've also managed to crash it in a similar way with ISOLDE's documentation (both are generated by Sphinx with the same template, so probably not surprising), but not with any ChimeraX docs. The new bundles with this documentation aren't up on the ToolShed yet, and I'm not sure it would be wise to put them there until this is fixed. Let me know if you need a copy of the wheel files to test locally. Program received signal SIGSEGV, Segmentation fault. 0x00007fffd55282dc in ?? () from /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5WebEngineCore.so.5 Missing separate debuginfos, use: debuginfo-install ucsf-chimerax-daily-2019.11.13-1.el7.x86_64 (gdb) bt #0 0x00007fffd55282dc in () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5WebEngineCore.so.5 #1 0x00007fffd552c08e in () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5WebEngineCore.so.5 #2 0x00007fffd5531614 in () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5WebEngineCore.so.5 #3 0x00007fffd551b424 in () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5WebEngineCore.so.5 #4 0x00007fffd48a6330 in QQuickWindowPrivate::updateDirtyNode(QQuickItem*) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Quick.so.5 #5 0x00007fffd48a6a1d in QQuickWindowPrivate::updateDirtyNodes() () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Quick.so.5 #6 0x00007fffd48a7bd2 in QQuickWindowPrivate::syncSceneGraph() () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Quick.so.5 #7 0x00007fffd4962a99 in QQuickRenderControl::sync() () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Quick.so.5 #8 0x00007fffd33241f0 in QQuickWidgetPrivate::render(bool) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5QuickWidgets.so.5 #9 0x00007fffd33242ae in QQuickWidgetPrivate::renderSceneGraph() () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5QuickWidgets.so.5 #10 0x00007fffdfcbe9db in QObject::event(QEvent*) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Core.so.5 #11 0x00007fffe0ba2fc3 in QWidget::event(QEvent*) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Widgets.so.5 #12 0x00007fffd3327dab in QQuickWidget::event(QEvent*) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5QuickWidgets.so.5 #13 0x00007fffdc0668b0 in QtWebEngineCore::RenderWidgetHostViewQtDelegateWidget::event(QEvent*) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5WebEngineWidgets.so.5 #14 0x00007fffe0b6492c in QApplicationPrivate::notify_helper(QObject*, QEvent*) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Widgets.so.5 #15 0x00007fffe0b6bad0 in QApplication::notify(QObject*, QEvent*) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Widgets.so.5 #16 0x00007fffe15bff5e in sipQApplication::notify(QObject*, QEvent*) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/QtWidgets.so #17 0x00007fffdfc92008 in QCoreApplication::notifyInternal2(QObject*, QEvent*) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Core.so.5 #18 0x00007fffdfce88d9 in QTimerInfoList::activateTimers() () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Core.so.5 #19 0x00007fffdfce90b1 in timerSourceDispatch(_GSource*, int (*)(void*), void*) () at /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Core.so.5 #20 0x00007fffdd31e049 in g_main_context_dispatch () at /lib64/libglib-2.0.so.0 Log: UCSF ChimeraX version: 0.91 (2019-11-13) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > usage clipper clipper associate volumes [toModel a structure specifier] — Have Clipper take control of the chosen volumes and associate them with the given model clipper isolate atoms [surroundDistance a number] [contextDistance a number] [maskRadius a number] [hideSurrounds true or false] [focus true or false] — Visually isolate the selected atoms from their surroundings, and mask their maps to their immediate vicinity. The selection covered by the map(s) will be expanded to include all residues approaching within surroundDistance of the given selection. Any residues approaching within contextDistance of the result will be displayed, but not covered by the map(s). If hideSurrounds is True, all other atoms will be hidden. If focus is True, the view will be reset to cover the visible atoms. To revert to the default viewing mode, use ""clipper spotlight"". clipper open path [structureModel a structure specifier] [overSampling a number] — Open a structure factor .mtz or .cif file and generate maps for the given model path: name of a file to open/read clipper save path [models] [preserveInput true or false] [saveMapCoeffs true or false] — Save structure factors to .mtz format. path: name of a file to save/write clipper spotlight [models] [radius a number] — Switch on/off ""Scrolling sphere"" visualisation with live atomic symmetry OpenGL version: 3.3.0 NVIDIA 415.27 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed major 1.0 Help System fixed all ChimeraX