id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3769 Graphics hardware encountered an error and was reset achitre22@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-19.5.0-x86_64-i386-64bit ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Process: ChimeraX [29065] Path: /Applications/ChimeraX-1.1.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.1.0 (1.1.0.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [29065] User ID: 501 Date/Time: 2020-09-29 09:39:01.666 -0700 OS Version: Mac OS X 10.15.5 (19F96) Report Version: 12 Bridge OS Version: 4.5 (17P5290) Anonymous UUID: AA91FA8B-0A8D-862D-FF09-8117DC28E3DD Sleep/Wake UUID: 0829E59A-E48B-4A21-A07C-FFAEA02D5410 Time Awake Since Boot: 280000 seconds Time Since Wake: 1100 seconds System Integrity Protection: enabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_CRASH (SIGABRT) Exception Codes: 0x0000000000000000, 0x0000000000000000 Exception Note: EXC_CORPSE_NOTIFY Application Specific Information: abort() called Application Specific Signatures: Graphics hardware encountered an error and was reset: 0x00000813 Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff7114c33a __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff71208e60 pthread_kill + 430 2 libsystem_c.dylib 0x00007fff7106393e raise + 26 3 libsystem_platform.dylib 0x00007fff711fd5fd _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 libsystem_c.dylib 0x00007fff710d3808 abort + 120 6 libGPUSupportMercury.dylib 0x00007fff584240a5 gpusGenerateCrashLog.cold.1 + 95 7 libGPUSupportMercury.dylib 0x00007fff5841b18f gpusGenerateCrashLog + 89 8 com.apple.driver.AppleIntelKBLGraphicsGLDriver 0x00007fff2f72df18 gpusKillClientExt + 9 9 libGPUSupportMercury.dylib 0x00007fff5841c6a1 gpusSubmitDataBuffers + 490 10 com.apple.driver.AppleIntelKBLGraphicsGLDriver 0x00007fff2e99a086 IntelCommandBuffer::getNew(GLDContextRec*) + 48 11 com.apple.driver.AppleIntelKBLGraphicsGLDriver 0x00007fff2e999e94 intelSubmitCommands + 171 12 com.apple.driver.AppleIntelKBLGraphicsGLDriver 0x00007fff2eac4d8a gldPresentFramebufferData + 120 13 GLEngine 0x00007fff41b298d1 glSwap_Exec + 97 14 com.apple.opengl 0x00007fff41b0b473 CGLFlushDrawable + 59 15 com.apple.AppKit 0x00007fff34628f2a -[NSOpenGLContext flushBuffer] + 20 16 libqcocoa.dylib 0x000000011b9cbd3d 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com.apple.CoreFoundation 0x00007fff37009b9b __CFRunLoopDoSources0 + 209 58 com.apple.CoreFoundation 0x00007fff370088ca __CFRunLoopRun + 927 59 com.apple.CoreFoundation 0x00007fff37007ece CFRunLoopRunSpecific + 462 60 com.apple.HIToolbox 0x00007fff35c36abd RunCurrentEventLoopInMode + 292 61 com.apple.HIToolbox 0x00007fff35c367d5 ReceiveNextEventCommon + 584 62 com.apple.HIToolbox 0x00007fff35c36579 _BlockUntilNextEventMatchingListInModeWithFilter + 64 63 com.apple.AppKit 0x00007fff3427e829 _DPSNextEvent + 883 64 com.apple.AppKit 0x00007fff3427d070 -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1352 65 com.apple.AppKit 0x00007fff3426ed7e -[NSApplication run] + 658 66 libqcocoa.dylib 0x000000011b9aade3 0x11b975000 + 220643 67 QtCore 0x0000000111d7893f QEventLoop::exec(QFlags) + 431 68 QtCore 0x0000000111d7d932 QCoreApplication::exec() + 130 69 QtWidgets.so 0x0000000110d407d2 meth_QApplication_exec_(_object*, _object*) + 82 70 org.python.python 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com.apple.CoreFoundation 0x00007fff37009f85 __CFRunLoopServiceMachPort + 247 3 com.apple.CoreFoundation 0x00007fff37008a52 __CFRunLoopRun + 1319 4 com.apple.CoreFoundation 0x00007fff37007ece CFRunLoopRunSpecific + 462 5 com.apple.AppKit 0x00007fff34420144 _NSEventThread + 132 6 libsystem_pthread.dylib 0x00007fff71209109 _pthread_start + 148 7 libsystem_pthread.dylib 0x00007fff71204b8b thread_start + 15 Thread 5:: NetworkConfigWatcher 0 libsystem_kernel.dylib 0x00007fff71145dfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff71146170 mach_msg + 60 2 QtWebEngineCore 0x000000011657a32d 0x1143d8000 + 35267373 3 QtWebEngineCore 0x000000011657a22f 0x1143d8000 + 35267119 4 QtWebEngineCore 0x000000011652e05d 0x1143d8000 + 34955357 5 QtWebEngineCore 0x0000000116557085 0x1143d8000 + 35123333 6 QtWebEngineCore 0x00000001165a99bc 0x1143d8000 + 35461564 7 QtWebEngineCore 0x00000001165e9717 0x1143d8000 + 35723031 8 libsystem_pthread.dylib 0x00007fff71209109 _pthread_start + 148 9 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0x0000000116598a74 0x1143d8000 + 35392116 6 QtWebEngineCore 0x00000001165a99bc 0x1143d8000 + 35461564 7 QtWebEngineCore 0x00000001165e9717 0x1143d8000 + 35723031 8 libsystem_pthread.dylib 0x00007fff71209109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff71204b8b thread_start + 15 Thread 8:: TaskSchedulerForegroundWorker 0 libsystem_kernel.dylib 0x00007fff71145dfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff71146170 mach_msg + 60 2 QtWebEngineCore 0x000000011657a32d 0x1143d8000 + 35267373 3 QtWebEngineCore 0x000000011657a421 0x1143d8000 + 35267617 4 QtWebEngineCore 0x0000000116591d28 0x1143d8000 + 35364136 5 QtWebEngineCore 0x000000011659265b 0x1143d8000 + 35366491 6 QtWebEngineCore 0x00000001165922c4 0x1143d8000 + 35365572 7 QtWebEngineCore 0x00000001165e9717 0x1143d8000 + 35723031 8 libsystem_pthread.dylib 0x00007fff71209109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff71204b8b thread_start + 15 Thread 9:: TaskSchedulerForegroundBlockingWorker 0 libsystem_kernel.dylib 0x00007fff71145dfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff71146170 mach_msg + 60 2 QtWebEngineCore 0x000000011657a32d 0x1143d8000 + 35267373 3 QtWebEngineCore 0x000000011657a421 0x1143d8000 + 35267617 4 QtWebEngineCore 0x0000000116591d28 0x1143d8000 + 35364136 5 QtWebEngineCore 0x000000011659265b 0x1143d8000 + 35366491 6 QtWebEngineCore 0x00000001165922c4 0x1143d8000 + 35365572 7 QtWebEngineCore 0x00000001165e9717 0x1143d8000 + 35723031 8 libsystem_pthread.dylib 0x00007fff71209109 _pthread_start + 148 9 libsystem_pthread.dylib 0x00007fff71204b8b thread_start + 15 Thread 10:: TaskSchedulerBackgroundWorker 0 libsystem_kernel.dylib 0x00007fff71145dfa mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff71146170 mach_msg + 60 2 QtWebEngineCore 0x000000011657a32d 0x1143d8000 + 35267373 3 QtWebEngineCore 0x000000011657a421 0x1143d8000 + 35267617 4 QtWebEngineCore 0x0000000116591d28 0x1143d8000 + 35364136 5 QtWebEngineCore 0x000000011659265b 0x1143d8000 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_PyObject_Call_Prepend + 131 25 org.python.python 0x0000000103e839f8 PyObject_Call + 136 26 org.python.python 0x0000000103fe9297 t_bootstrap + 71 27 org.python.python 0x0000000103f9cd29 pythread_wrapper + 25 28 libsystem_pthread.dylib 0x00007fff71209109 _pthread_start + 148 29 libsystem_pthread.dylib 0x00007fff71204b8b thread_start + 15 Thread 24: 0 libsystem_pthread.dylib 0x00007fff71204b68 start_wqthread + 0 Thread 25: 0 libsystem_pthread.dylib 0x00007fff71204b68 start_wqthread + 0 Thread 26: 0 libsystem_pthread.dylib 0x00007fff71204b68 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000000010cad3dc0 rcx: 0x00007fde52e77a58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x0000000000000006 rbp: 0x00007fde52e77a80 rsp: 0x00007fde52e77a58 r8: 0x00007fde52e77f48 r9: 0xa8484ff0d2e4e836 r10: 0x000000010cad3dc0 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x00007fde5669c518 r14: 0x0000000000000006 r15: 0x0000000000000016 rip: 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/usr/lib/libMobileGestalt.dylib 0x7fff6def8000 - 0x7fff6dfd5ff7 libSMC.dylib (20) /usr/lib/libSMC.dylib 0x7fff6dfea000 - 0x7fff6dfebfff libSystem.B.dylib (1281.100.1) /usr/lib/libSystem.B.dylib 0x7fff6dfec000 - 0x7fff6e077ff7 libTelephonyUtilDynamic.dylib (5017.1) /usr/lib/libTelephonyUtilDynamic.dylib 0x7fff6e078000 - 0x7fff6e079fff libThaiTokenizer.dylib (3) /usr/lib/libThaiTokenizer.dylib 0x7fff6e091000 - 0x7fff6e0a7fff libapple_nghttp2.dylib (1.39.2) /usr/lib/libapple_nghttp2.dylib 0x7fff6e0dc000 - 0x7fff6e14eff7 libarchive.2.dylib (72.100.1) /usr/lib/libarchive.2.dylib 0x7fff6e14f000 - 0x7fff6e1e8fe5 libate.dylib (3.0.1) /usr/lib/libate.dylib 0x7fff6e1ec000 - 0x7fff6e1ecff3 libauto.dylib (187) /usr/lib/libauto.dylib 0x7fff6e1ed000 - 0x7fff6e2b1ffe libboringssl.dylib (283.120.1) /usr/lib/libboringssl.dylib 0x7fff6e2b2000 - 0x7fff6e2c2ffb libbsm.0.dylib (60.100.1) /usr/lib/libbsm.0.dylib 0x7fff6e2c3000 - 0x7fff6e2cffff libbz2.1.0.dylib (44) /usr/lib/libbz2.1.0.dylib 0x7fff6e2d0000 - 0x7fff6e322fff libc++.1.dylib (902.1) /usr/lib/libc++.1.dylib 0x7fff6e323000 - 0x7fff6e338ffb libc++abi.dylib (902) /usr/lib/libc++abi.dylib 0x7fff6e339000 - 0x7fff6e339fff libcharset.1.dylib (59) /usr/lib/libcharset.1.dylib 0x7fff6e33a000 - 0x7fff6e34bfff libcmph.dylib (8) /usr/lib/libcmph.dylib 0x7fff6e34c000 - 0x7fff6e363fd7 libcompression.dylib (87) /usr/lib/libcompression.dylib 0x7fff6e63d000 - 0x7fff6e653ff7 libcoretls.dylib (167) /usr/lib/libcoretls.dylib 0x7fff6e654000 - 0x7fff6e655fff libcoretls_cfhelpers.dylib (167) /usr/lib/libcoretls_cfhelpers.dylib 0x7fff6eaf8000 - 0x7fff6ebfcfef libcrypto.44.dylib (47.120.1) /usr/lib/libcrypto.44.dylib 0x7fff6ebff000 - 0x7fff6ec0afff libcsfde.dylib (551) /usr/lib/libcsfde.dylib 0x7fff6ec12000 - 0x7fff6ec71ff7 libcups.2.dylib (483.6) /usr/lib/libcups.2.dylib 0x7fff6ec73000 - 0x7fff6ecd8ff7 libcurl.4.dylib (118.120.2) /usr/lib/libcurl.4.dylib 0x7fff6ed7b000 - 0x7fff6ed7bfff libenergytrace.dylib (21) /usr/lib/libenergytrace.dylib 0x7fff6ed7c000 - 0x7fff6ed94fff libexpat.1.dylib (19.60.2) /usr/lib/libexpat.1.dylib 0x7fff6eda2000 - 0x7fff6eda4fff libfakelink.dylib (149.1) /usr/lib/libfakelink.dylib 0x7fff6edb3000 - 0x7fff6edb8fff libgermantok.dylib (24) /usr/lib/libgermantok.dylib 0x7fff6edb9000 - 0x7fff6edc2ff7 libheimdal-asn1.dylib (564.100.1) /usr/lib/libheimdal-asn1.dylib 0x7fff6edc3000 - 0x7fff6eeb3fff libiconv.2.dylib (59) /usr/lib/libiconv.2.dylib 0x7fff6eeb4000 - 0x7fff6f10bfff libicucore.A.dylib (64260.0.1) /usr/lib/libicucore.A.dylib 0x7fff6f125000 - 0x7fff6f126fff liblangid.dylib (133) /usr/lib/liblangid.dylib 0x7fff6f127000 - 0x7fff6f13fff3 liblzma.5.dylib (16) /usr/lib/liblzma.5.dylib 0x7fff6f157000 - 0x7fff6f1feff7 libmecab.dylib (883.11) /usr/lib/libmecab.dylib 0x7fff6f1ff000 - 0x7fff6f461ff1 libmecabra.dylib (883.11) /usr/lib/libmecabra.dylib 0x7fff6f7ce000 - 0x7fff6f7fdfff libncurses.5.4.dylib (57) /usr/lib/libncurses.5.4.dylib 0x7fff6f92d000 - 0x7fff6fda9ff5 libnetwork.dylib (1880.120.4) /usr/lib/libnetwork.dylib 0x7fff6fdaa000 - 0x7fff6fdc1fff libnetworkextension.dylib (1095.120.6) /usr/lib/libnetworkextension.dylib 0x7fff6fe4a000 - 0x7fff6fe7dfde libobjc.A.dylib (787.1) /usr/lib/libobjc.A.dylib 0x7fff6fe7e000 - 0x7fff6fe7fff7 libodfde.dylib (26) /usr/lib/libodfde.dylib 0x7fff6fe90000 - 0x7fff6fe94fff libpam.2.dylib (25.100.1) /usr/lib/libpam.2.dylib 0x7fff6fe97000 - 0x7fff6fecdff7 libpcap.A.dylib (89.120.1) /usr/lib/libpcap.A.dylib 0x7fff6ff0d000 - 0x7fff6ff1bff9 libperfcheck.dylib (37.100.2) /usr/lib/libperfcheck.dylib 0x7fff6ff51000 - 0x7fff6ff69fff libresolv.9.dylib (67.40.1) /usr/lib/libresolv.9.dylib 0x7fff6ff6b000 - 0x7fff6ffafff7 libsandbox.1.dylib (1217.120.7) /usr/lib/libsandbox.1.dylib 0x7fff6ffb0000 - 0x7fff6ffc2ff7 libsasl2.2.dylib (213.120.1) /usr/lib/libsasl2.2.dylib 0x7fff6ffc3000 - 0x7fff6ffc4ff7 libspindump.dylib (281.3) /usr/lib/libspindump.dylib 0x7fff6ffc5000 - 0x7fff701afff7 libsqlite3.dylib (308.5) /usr/lib/libsqlite3.dylib 0x7fff702a3000 - 0x7fff702d0ffb libssl.46.dylib (47.120.1) /usr/lib/libssl.46.dylib 0x7fff703a5000 - 0x7fff703ffff8 libusrtcp.dylib (1880.120.4) /usr/lib/libusrtcp.dylib 0x7fff70400000 - 0x7fff70403ffb libutil.dylib (57) /usr/lib/libutil.dylib 0x7fff70404000 - 0x7fff70411ff7 libxar.1.dylib (425.2) /usr/lib/libxar.1.dylib 0x7fff70417000 - 0x7fff704f9ff7 libxml2.2.dylib (33.3) /usr/lib/libxml2.2.dylib 0x7fff704fd000 - 0x7fff70525fff libxslt.1.dylib (16.9) /usr/lib/libxslt.1.dylib 0x7fff70526000 - 0x7fff70538ff3 libz.1.dylib (76) /usr/lib/libz.1.dylib 0x7fff70de6000 - 0x7fff70debff3 libcache.dylib (83) /usr/lib/system/libcache.dylib 0x7fff70dec000 - 0x7fff70df7fff libcommonCrypto.dylib (60165.120.1) /usr/lib/system/libcommonCrypto.dylib 0x7fff70df8000 - 0x7fff70dfffff libcompiler_rt.dylib (101.2) /usr/lib/system/libcompiler_rt.dylib 0x7fff70e00000 - 0x7fff70e09ff7 libcopyfile.dylib (166.40.1) /usr/lib/system/libcopyfile.dylib 0x7fff70e0a000 - 0x7fff70e9cfe3 libcorecrypto.dylib (866.120.3) /usr/lib/system/libcorecrypto.dylib 0x7fff70fa9000 - 0x7fff70fe9ff0 libdispatch.dylib (1173.100.2) /usr/lib/system/libdispatch.dylib 0x7fff70fea000 - 0x7fff71020fff libdyld.dylib (750.5) /usr/lib/system/libdyld.dylib 0x7fff71021000 - 0x7fff71021ffb libkeymgr.dylib (30) /usr/lib/system/libkeymgr.dylib 0x7fff71022000 - 0x7fff7102eff3 libkxld.dylib (6153.121.1) /usr/lib/system/libkxld.dylib 0x7fff7102f000 - 0x7fff7102fff7 liblaunch.dylib (1738.120.8) /usr/lib/system/liblaunch.dylib 0x7fff71030000 - 0x7fff71035ff7 libmacho.dylib (959.0.1) /usr/lib/system/libmacho.dylib 0x7fff71036000 - 0x7fff71038ff3 libquarantine.dylib (110.40.3) /usr/lib/system/libquarantine.dylib 0x7fff71039000 - 0x7fff7103aff7 libremovefile.dylib (48) /usr/lib/system/libremovefile.dylib 0x7fff7103b000 - 0x7fff71052ff3 libsystem_asl.dylib (377.60.2) /usr/lib/system/libsystem_asl.dylib 0x7fff71053000 - 0x7fff71053ff7 libsystem_blocks.dylib (74) /usr/lib/system/libsystem_blocks.dylib 0x7fff71054000 - 0x7fff710dbfff libsystem_c.dylib (1353.100.2) /usr/lib/system/libsystem_c.dylib 0x7fff710dc000 - 0x7fff710dfffb libsystem_configuration.dylib (1061.120.2) /usr/lib/system/libsystem_configuration.dylib 0x7fff710e0000 - 0x7fff710e3fff libsystem_coreservices.dylib (114) /usr/lib/system/libsystem_coreservices.dylib 0x7fff710e4000 - 0x7fff710ecfff libsystem_darwin.dylib (1353.100.2) /usr/lib/system/libsystem_darwin.dylib 0x7fff710ed000 - 0x7fff710f4fff libsystem_dnssd.dylib (1096.100.3) /usr/lib/system/libsystem_dnssd.dylib 0x7fff710f5000 - 0x7fff710f6ffb libsystem_featureflags.dylib (17) /usr/lib/system/libsystem_featureflags.dylib 0x7fff710f7000 - 0x7fff71144ff7 libsystem_info.dylib (538) /usr/lib/system/libsystem_info.dylib 0x7fff71145000 - 0x7fff71171ff7 libsystem_kernel.dylib (6153.121.1) /usr/lib/system/libsystem_kernel.dylib 0x7fff71172000 - 0x7fff711b9fff libsystem_m.dylib (3178) /usr/lib/system/libsystem_m.dylib 0x7fff711ba000 - 0x7fff711e1fff libsystem_malloc.dylib (283.100.6) /usr/lib/system/libsystem_malloc.dylib 0x7fff711e2000 - 0x7fff711efffb libsystem_networkextension.dylib (1095.120.6) /usr/lib/system/libsystem_networkextension.dylib 0x7fff711f0000 - 0x7fff711f9ff7 libsystem_notify.dylib (241.100.2) /usr/lib/system/libsystem_notify.dylib 0x7fff711fa000 - 0x7fff71202fef libsystem_platform.dylib (220.100.1) /usr/lib/system/libsystem_platform.dylib 0x7fff71203000 - 0x7fff7120dfff libsystem_pthread.dylib (416.100.3) /usr/lib/system/libsystem_pthread.dylib 0x7fff7120e000 - 0x7fff71212ff3 libsystem_sandbox.dylib (1217.120.7) /usr/lib/system/libsystem_sandbox.dylib 0x7fff71213000 - 0x7fff71215fff libsystem_secinit.dylib (62.100.2) /usr/lib/system/libsystem_secinit.dylib 0x7fff71216000 - 0x7fff7121dffb libsystem_symptoms.dylib (1238.120.1) /usr/lib/system/libsystem_symptoms.dylib 0x7fff7121e000 - 0x7fff71234ff2 libsystem_trace.dylib (1147.120) /usr/lib/system/libsystem_trace.dylib 0x7fff71236000 - 0x7fff7123bff7 libunwind.dylib (35.4) /usr/lib/system/libunwind.dylib 0x7fff7123c000 - 0x7fff71271ffe libxpc.dylib (1738.120.8) /usr/lib/system/libxpc.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 31 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 302947 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=940.3M resident=0K(0%) swapped_out_or_unallocated=940.3M(100%) Writable regions: Total=1.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.0G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 512K 4 Activity Tracing 256K 1 CG backing stores 2332K 9 CG image 1176K 30 CoreAnimation 184K 35 CoreGraphics 8K 1 CoreImage 44K 7 CoreUI image data 2256K 31 Foundation 4K 1 Kernel Alloc Once 8K 1 MALLOC 295.6M 336 MALLOC guard page 32K 8 MALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) Memory Tag 242 12K 1 OpenGL GLSL 512K 6 PROTECTED_MEMORY 4K 1 STACK GUARD 104K 26 Stack 153.2M 27 Stack Guard 56.0M 1 VM_ALLOCATE 165.1M 350 VM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated) __DATA 51.7M 551 __DATA_CONST 44K 4 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 413.6M 143 __OBJC_RO 32.2M 1 __OBJC_RW 1892K 2 __TEXT 526.8M 512 __UNICODE 564K 1 mapped file 96.6M 64 shared memory 672K 20 =========== ======= ======= TOTAL 2.2G 2179 TOTAL, minus reserved VM space 1.8G 2179 Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1FB7 1fb7 title: Crystal structure of an In vivo hiv-1 protease mutant In complex with saquinavir: insights INTO the mechanisms of drug resistance [more info...] Chain information for 1fb7 #1 --- Chain | Description A | hiv-1 protease Non-standard residues in 1fb7 #1 --- ROC — (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert- butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1-phenyl- butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide (Fortovase; SAQUINAVIR,RO 31-8959) 1fb7 mmCIF Assemblies --- 1| author_and_software_defined_assembly > set bgColor white > select ::name=""CYS"" 12 atoms, 10 bonds, 2 residues, 1 model selected > open 6lu7 6lu7 title: The crystal structure of COVID-19 main protease in complex with an inhibitor N3 [more info...] Chain information for 6lu7 #2 --- Chain | Description A | main protease C | N-[(5-methylisoxazol-3-yl)carbonyl]alanyl-L- valyl-N~1~-((1R,2Z)-4-(benzyloxy)-4-oxo-1-{[(3R)-2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-L-leucinamide Non-standard residues in 6lu7 #2 --- 010 — phenylmethanol 02J — 5-methyl-1,2-oxazole-3-carboxylic acid PJE — (E,4S)-4-azanyl-5-[(3S)-2-oxidanylidenepyrrolidin-3-yl]pent-2-enoic acid 6lu7 mmCIF Assemblies --- 1| author_and_software_defined_assembly > close #1 > select ::name=""CYS"" 72 atoms, 60 bonds, 12 residues, 1 model selected > select /A 2451 atoms, 2420 bonds, 390 residues, 1 model selected > color sel cornflower blue > select /C 49 atoms, 51 bonds, 6 residues, 1 model selected > color sel hot pink > show sel atoms > color sel byhetero > select /A 2451 atoms, 2420 bonds, 390 residues, 1 model selected > select ::name=""CYS"" 72 atoms, 60 bonds, 12 residues, 1 model selected > show sel atoms > color sel byhetero > select ::name=""HIS"" 70 atoms, 71 bonds, 7 residues, 1 model selected > select clear > select /A:41 10 atoms, 10 bonds, 1 residue, 1 model selected > color sel byhetero > show sel atoms > ui tool show ""Side View"" > color sel orange > color sel byhetero > select clear > select /A:41@CB 1 atom, 1 residue, 1 model selected > ui tool show Distances > distance /A:41@CB /A:145@CB Distance between /A HIS 41 CB and CYS 145 CB: 7.419Å Must select one or more distances in the table > ~distance /A:41@CB /A:145@CB > select /A:41@CE1 1 atom, 1 residue, 1 model selected > select /A:145@CB 1 atom, 1 residue, 1 model selected > ui tool show Distances Exactly two atoms must be selected! > ui tool show Distances > distance /A:41@CE1 /A:145@CB Distance between /A HIS 41 CE1 and CYS 145 CB: 4.202Å > select /A:41@NE2 1 atom, 1 residue, 1 model selected > ui tool show Distances > distance /A:41@NE2 /A:145@CB Distance between /A HIS 41 NE2 and CYS 145 CB: 3.817Å OpenGL version: 4.1 INTEL-14.6.18 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB Boot ROM Version: 1037.120.87.0.0 (iBridge: 17.16.15290.0.0,0) Software: System Software Overview: System Version: macOS 10.15.5 (19F96) Kernel Version: Darwin 19.5.0 Time since boot: 6 days 14:21 Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal HP 23er: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60 Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 3CM015127T Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.0 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.0 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect closed normal Graphics nonchimerax all ChimeraX