id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16782 Crash opening PDB file chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff8535717c0 (most recent call first): File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/pdb/pdb.py"", line 74 in open_pdb File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/pdb/__init__.py"", line 34 in open File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/open_command/cmd.py"", line 421 in collated_open File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/open_command/cmd.py"", line 179 in provider_open File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py"", line 2852 in run File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/open_command/cmd.py"", line 118 in cmd_open File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/cli.py"", line 2852 in run File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/core/commands/run.py"", line 36 in run File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 1812 in _open_dropped_file File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 261 in event File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 293 in event_loop File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py"", line 866 in init File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py"", line 1015 in File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/runpy.py"", line 194 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2025-02-04 14:16:23.00 -0500"",""app_version"":""1.2.5"",""slice_uuid"":""74b1c996-e1f3-331c-8c86-116411356099"",""build_version"":""1.2.5.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.6.9 (22G830)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""E2CB1C7A-7F11-407B-B837-529721CF53B9""} { ""uptime"" : 61000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 1729161551, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,1"", ""coalitionID"" : 793, ""osVersion"" : { ""train"" : ""macOS 13.6.9"", ""build"" : ""22G830"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-02-04 14:16:21.2654 -0500"", ""incident"" : ""E2CB1C7A-7F11-407B-B837-529721CF53B9"", ""pid"" : 38482, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-02-03 14:00:42.2872 -0500"", ""procStartAbsTime"" : 29930210749599, ""procExitAbsTime"" : 61325821925134, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.2.5.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.2.5"",""CFBundleVersion"":""1.2.5.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""6830EE0E-B55D-5100-A30D-5FA572EA2E6C"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""B597D627-ED95-B146-ACA4-845EFB8FD215"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 19451, ""bridgeVersion"" : {""build"":""21P6074"",""train"":""8.6""}, ""sleepWakeUUID"" : ""ABE3416D-5F68-4E77-B869-608DCB05E441"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x8 is not in any region. 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(2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/sharmad4/Downloads/3qx3.pdb 3qx3.pdb title: Human topoisomerase iibeta In complex with DNA and etoposide [more info...] Chain information for 3qx3.pdb #1 --- Chain | Description A B | DNA topoisomerase 2-β C E | DNA (5'-D(P*ap*GP*CP*CP*GP*ap*GP*C)-3') D F | DNA (5'-D(P*TP*GP*CP*ap*GP*CP*TP*CP*GP*GP*CP*T)-3') Non-standard residues in 3qx3.pdb #1 --- EVP — (5S,5AR,8AR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5A,6,8,8A,9-hexahydrofuro[3',4':6,7]naphtho[2,3-D][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-β-D-glucopyranoside (etoposide; VP-16) MG — magnesium ion > open /Users/sharmad4/Downloads/3qx3.pdb 3qx3.pdb title: Human topoisomerase iibeta In complex with DNA and etoposide [more info...] Chain information for 3qx3.pdb #2 --- Chain | Description A B | DNA topoisomerase 2-β C E | DNA (5'-D(P*ap*GP*CP*CP*GP*ap*GP*C)-3') D F | DNA (5'-D(P*TP*GP*CP*ap*GP*CP*TP*CP*GP*GP*CP*T)-3') Non-standard residues in 3qx3.pdb #2 --- EVP — (5S,5AR,8AR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5A,6,8,8A,9-hexahydrofuro[3',4':6,7]naphtho[2,3-D][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-β-D-glucopyranoside (etoposide; VP-16) MG — magnesium ion OpenGL version: 4.1 ATI-4.14.1 OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0) OS Loader Version: 577.140.2~22 Software: System Software Overview: System Version: macOS 13.6.9 (22G830) Kernel Version: Darwin 22.6.0 Time since boot: 4 days, 5 hours, 21 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Radeon Pro 560X: Chipset Model: Radeon Pro 560X Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c2 ROM Revision: 113-C980AL-075 VBIOS Version: 113-C97501U-005 EFI Driver Version: 01.A1.075 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 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numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Input/Output can't reproduce all ChimeraX