id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8455 Crash in garbage collection hyli.pasteur@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-20.3.0-x86_64-i386-64bit ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Process: ChimeraX [1656] Path: /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX Identifier: edu.ucsf.cgl.ChimeraX Version: 1.1.1 (1.1.1.0) Code Type: X86-64 (Native) Parent Process: ??? [1] Responsible: ChimeraX [1656] User ID: 502 Date/Time: 2023-02-07 15:01:15.978 -0800 OS Version: macOS 11.2.3 (20D91) Report Version: 12 Anonymous UUID: B79D706D-003A-84DD-775C-D1F559EF1D49 Time Awake Since Boot: 450000 seconds System Integrity Protection: enabled Crashed Thread: 0 CrBrowserMain Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x00000000000000a9 Exception Note: EXC_CORPSE_NOTIFY VM Regions Near 0xa9: --> __TEXT 103d90000-103d91000 [ 4K] r-x/r-x SM=COW /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX Thread 0 Crashed:: CrBrowserMain Dispatch queue: com.apple.main-thread 0 libsystem_kernel.dylib 0x00007fff20471462 __pthread_kill + 10 1 libsystem_pthread.dylib 0x00007fff2049f610 pthread_kill + 263 2 libsystem_c.dylib 0x00007fff20381ba3 raise + 26 3 libsystem_platform.dylib 0x00007fff204e3d7d _sigtramp + 29 4 ??? 000000000000000000 0 + 0 5 org.python.python 0x0000000103e08980 tupletraverse + 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0x00000001056bac05 blas_thread_server + 565 3 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15 Thread 19: 0 libsystem_kernel.dylib 0x00007fff2046d8e2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff2049fe6f _pthread_cond_wait + 1254 2 libopenblasp-r0.3.7.dylib 0x00000001056bac3b blas_thread_server + 619 3 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224 4 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15 Thread 20:: TaskSchedulerBackgroundBlockingWorker 0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60 2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373 3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617 4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136 5 QtWebEngineCore 0x000000011657665b 0x1143bc000 + 35366491 6 QtWebEngineCore 0x0000000116576234 0x1143bc000 + 35365428 7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031 8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15 Thread 21:: QFileInfoGatherer 0 libsystem_kernel.dylib 0x00007fff2046d8e2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff2049fe6f _pthread_cond_wait + 1254 2 QtCore 0x00000001119488ab 0x11191e000 + 174251 3 QtCore 0x000000011194880c QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 4 QtWidgets 0x0000000111047762 0x110e0c000 + 2340706 5 QtCore 0x00000001119400b3 0x11191e000 + 139443 6 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15 Thread 22: 0 libsystem_pthread.dylib 0x00007fff2049b458 start_wqthread + 0 Thread 23: 0 libsystem_pthread.dylib 0x00007fff2049b458 start_wqthread + 0 Thread 24:: QFileInfoGatherer 0 libsystem_kernel.dylib 0x00007fff2046d8e2 __psynch_cvwait + 10 1 libsystem_pthread.dylib 0x00007fff2049fe6f _pthread_cond_wait + 1254 2 QtCore 0x00000001119488ab 0x11191e000 + 174251 3 QtCore 0x000000011194880c QWaitCondition::wait(QMutex*, QDeadlineTimer) + 108 4 QtWidgets 0x0000000111047762 0x110e0c000 + 2340706 5 QtCore 0x00000001119400b3 0x11191e000 + 139443 6 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224 7 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15 Thread 25: 0 libsystem_pthread.dylib 0x00007fff2049b458 start_wqthread + 0 Thread 26:: TaskSchedulerBackgroundBlockingWorker 0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60 2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373 3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617 4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136 5 QtWebEngineCore 0x000000011657665b 0x1143bc000 + 35366491 6 QtWebEngineCore 0x0000000116576234 0x1143bc000 + 35365428 7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031 8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15 Thread 27:: TaskSchedulerForegroundWorker 0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60 2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373 3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617 4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136 5 QtWebEngineCore 0x00000001165763bf 0x1143bc000 + 35365823 6 QtWebEngineCore 0x00000001165762c4 0x1143bc000 + 35365572 7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031 8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15 Thread 28:: TaskSchedulerBackgroundBlockingWorker 0 libsystem_kernel.dylib 0x00007fff2046ae7e mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff2046b1f0 mach_msg + 60 2 QtWebEngineCore 0x000000011655e32d 0x1143bc000 + 35267373 3 QtWebEngineCore 0x000000011655e421 0x1143bc000 + 35267617 4 QtWebEngineCore 0x0000000116575d28 0x1143bc000 + 35364136 5 QtWebEngineCore 0x000000011657665b 0x1143bc000 + 35366491 6 QtWebEngineCore 0x0000000116576234 0x1143bc000 + 35365428 7 QtWebEngineCore 0x00000001165cd717 0x1143bc000 + 35723031 8 libsystem_pthread.dylib 0x00007fff2049f950 _pthread_start + 224 9 libsystem_pthread.dylib 0x00007fff2049b47b thread_start + 15 Thread 29: 0 libsystem_pthread.dylib 0x00007fff2049b458 start_wqthread + 0 Thread 30: 0 libsystem_pthread.dylib 0x00007fff2049b458 start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0000000000000000 rbx: 0x000000010bf51e00 rcx: 0x00007fbdd805fa58 rdx: 0x0000000000000000 rdi: 0x0000000000000307 rsi: 0x000000000000000b rbp: 0x00007fbdd805fa80 rsp: 0x00007fbdd805fa58 r8: 0x00007fbdd805ff48 r9: 0xc19c27be4b361c66 r10: 0x000000010bf51e00 r11: 0x0000000000000246 r12: 0x0000000000000307 r13: 0x000000012bc61320 r14: 0x000000000000000b r15: 0x0000000000000016 rip: 0x00007fff20471462 rfl: 0x0000000000000246 cr2: 0x0000000103ff8fa4 Logical CPU: 0 Error Code: 0x02000148 Trap Number: 133 Thread 0 instruction stream: 48 8b 40 18 4a 8b 1c e8-48 ff 03 48 89 df 4c 89 H.@.J...H..H..L. fe 4c 89 f2 4c 89 e1 31-c0 e8 72 e9 ec ff 48 85 .L..L..1..r...H. c0 74 9d 48 ff 08 74 b8-48 ff 0b 74 a0 49 ff c5 .t.H..t.H..t.I.. 48 8d 05 39 a0 12 00 48-8b 80 88 02 00 00 4c 3b H..9...H......L; 68 10 7c bc 49 ff 0c 24-74 24 48 83 c4 08 5b 41 h.|.I..$t$H...[A 5c 41 5d 41 5e 41 5f 5d-c3 31 ff 48 83 c4 08 5b \A]A^A_].1.H...[ 41 5c 41 5d 41 5e 41 5f-5d e9 f2 8e fb ff 49 8b A\A]A^A_].....I. 44 24 08 4c 89 e7 48 83-c4 08 5b 41 5c 41 5d 41 D$.L..H...[A\A]A 5e 41 5f 5d ff 60 30 66-0f 1f 84 00 00 00 00 00 ^A_].`0f........ 55 48 89 e5 53 50 48 8b-47 08[f6]80 a9 00 00 00 UH..SPH.G....... /Applications/ChimeraX-1.1.1.app/Contents/MacOS/ChimeraX 0x103d9a000 - 0x103f95fff +org.python.python (3.7.8, [c] 2001-2019 Python Software Foundation. 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/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_lzma.cpython-37m-darwin.so 0x104464000 - 0x104464fff +grp.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/grp.cpython-37m-darwin.so 0x1044ac000 - 0x1044b1fff +math.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/math.cpython-37m-darwin.so 0x1044bd000 - 0x1044bffff +_hashlib.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_hashlib.cpython-37m-darwin.so 0x1044c9000 - 0x104526fff +libssl.1.1.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/libssl.1.1.dylib 0x104555000 - 0x10471cfff +libcrypto.1.1.dylib (0) /Applications/ChimeraX-1.1.1.app/Contents/lib/libcrypto.1.1.dylib 0x1047b5000 - 0x1047bafff +_blake2.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_blake2.cpython-37m-darwin.so 0x1047c4000 - 0x1047d4fff +_sha3.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_sha3.cpython-37m-darwin.so 0x1047df000 - 0x1047dffff +_bisect.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_bisect.cpython-37m-darwin.so 0x1047e7000 - 0x1047e8fff +_random.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_random.cpython-37m-darwin.so 0x1048b0000 - 0x1048b6fff +_json.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_json.cpython-37m-darwin.so 0x1048ff000 - 0x10490cfff +_ssl.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_ssl.cpython-37m-darwin.so 0x104922000 - 0x10492bfff +_socket.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_socket.cpython-37m-darwin.so 0x10497d000 - 0x104980fff +select.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/select.cpython-37m-darwin.so 0x10498b000 - 0x10498ffff +_struct.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_struct.cpython-37m-darwin.so 0x10499d000 - 0x1049a1fff 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/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/pyexpat.cpython-37m-darwin.so 0x104bf7000 - 0x104bf8fff +_queue.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_queue.cpython-37m-darwin.so 0x104cc1000 - 0x104cc2fff +_posixsubprocess.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_posixsubprocess.cpython-37m-darwin.so 0x104d0a000 - 0x104d1cfff +_pickle.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_pickle.cpython-37m-darwin.so 0x104d6d000 - 0x104d70fff +_csv.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/lib-dynload/_csv.cpython-37m-darwin.so 0x104efb000 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/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/fft/_pocketfft_internal.cpython-37m-darwin.so 0x10b6c9000 - 0x10b734fff +mtrand.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/mtrand.cpython-37m-darwin.so 0x10b78f000 - 0x10b7acfff +_bit_generator.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_bit_generator.cpython-37m-darwin.so 0x10b7cd000 - 0x10b7fcfff +_common.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_common.cpython-37m-darwin.so 0x10b817000 - 0x10b86bfff +_bounded_integers.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_bounded_integers.cpython-37m-darwin.so 0x10b893000 - 0x10b8a5fff +_mt19937.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_mt19937.cpython-37m-darwin.so 0x10b8b6000 - 0x10b8c2fff +_philox.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_philox.cpython-37m-darwin.so 0x10b8d2000 - 0x10b8dcfff +_pcg64.cpython-37m-darwin.so (0) /Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/numpy/random/_pcg64.cpython-37m-darwin.so 0x10b8ec000 - 0x10b8f3fff +_sfc64.cpython-37m-darwin.so (0) 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0x7fff6ca09fff com.apple.opengl (18.1.1 - 18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL 0x7fff6ca0a000 - 0x7fff6ca0cfff libCVMSPluginSupport.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib 0x7fff6ca0d000 - 0x7fff6ca15fff libGFXShared.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib 0x7fff6ca16000 - 0x7fff6ca49fff libGLImage.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib 0x7fff6ca4a000 - 0x7fff6ca86fff libGLU.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib 0x7fff6ca87000 - 0x7fff6cc1bfff libGLProgrammability.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib 0x7fff6cc1c000 - 0x7fff6cc26fff libGL.dylib (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x7fff6cc27000 - 0x7fff6cda2fff GLEngine (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine 0x7fff6cda3000 - 0x7fff6cdccfff GLRendererFloat (18.1.1) /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat 0x7fff6e05d000 - 0x7fff6e0b5fff com.apple.opencl (4.5 - 4.5) /System/Library/Frameworks/OpenCL.framework/Versions/A/OpenCL 0x7fff6ebff000 - 0x7fff6edbffff com.apple.AMDMTLBronzeDriver (4.2.15 - 4.0.2) /System/Library/Extensions/AMDMTLBronzeDriver.bundle/Contents/MacOS/AMDMTLBronzeDriver 0x7fff6ef38000 - 0x7fff6ef87fff ATIRadeonX4000SCLib.dylib (4.2.15) /System/Library/Extensions/AMDRadeonX4000GLDriver.bundle/Contents/MacOS/ATIRadeonX4000SCLib.dylib 0x7fff6f134000 - 0x7fff6f13bfff com.apple.agl (3.3.4 - AGL-3.3.3) /System/Library/Frameworks/AGL.framework/Versions/A/AGL 0x7fff744ca000 - 0x7fff744d5fff com.apple.SymptomAnalytics (1.0 - 1431.40.36) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomAnalytics.framework/Versions/A/SymptomAnalytics 0x7fff746f3000 - 0x7fff7470bfff com.apple.SymptomPresentationFeed (1.0 - 1431.40.36) /System/Library/PrivateFrameworks/Symptoms.framework/Frameworks/SymptomPresentationFeed.framework/Versions/A/SymptomPresentationFeed 0x7fff78222000 - 0x7fff78229fff libRosetta.dylib (203.30) /usr/lib/libRosetta.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 11 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: 354607 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.0G resident=0K(0%) swapped_out_or_unallocated=1.0G(100%) Writable regions: Total=2.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.3G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 256K 2 Activity Tracing 256K 1 CG backing stores 4608K 6 CG image 700K 33 CG raster data 316K 1 CoreAnimation 2060K 27 CoreGraphics 12K 2 CoreServices 624K 2 CoreUI image data 4220K 33 Foundation 36K 2 Kernel Alloc Once 8K 1 MALLOC 1.3G 132 MALLOC guard page 48K 10 MALLOC_LARGE (reserved) 24.6M 2 reserved VM address space (unallocated) MALLOC_MEDIUM (reserved) 336.0M 4 reserved VM address space (unallocated) MALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated) OpenGL GLSL 512K 6 PROTECTED_MEMORY 4K 1 STACK GUARD 120K 30 Stack 165.7M 31 Stack Guard 56.0M 1 VM_ALLOCATE 234.3M 500 __CTF 759 1 __DATA 41.3M 596 __DATA_CONST 21.0M 268 __DATA_DIRTY 1191K 165 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 513.9M 145 __OBJC_RO 60.5M 1 __OBJC_RW 2449K 2 __TEXT 537.1M 571 __UNICODE 588K 1 mapped file 261.6M 45 shared memory 48K 6 =========== ======= ======= TOTAL 3.8G 2631 TOTAL, minus reserved VM space 3.2G 2631 Log: UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/haoyang/Google_Drive_LJI/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/NativeGP_April15_2022_glycans_2510C.cxs Log from Wed May 25 10:47:48 2022UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/CysRRLL_INOG_WT_NSEM.cxs"" Log from Thu Apr 14 17:05:32 2022UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open > /Users/haoyang/Google_Drive_LJI/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/CysRRLL_INOG_WT_NSEM.cxs Log from Tue Apr 12 22:31:49 2022UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSEM.cxs"" format session Log from Tue Apr 12 22:19:12 2022UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/haoyangli/Downloads/cryosparc_P34_J338_003_volume_map.mrc Opened cryosparc_P34_J338_003_volume_map.mrc, grid size 256,256,256, pixel 1.7, shown at level 0.0358, step 1, values float32 > volume #1 level 0.132 > lighting soft > vop gaussian #1 sdev 5.1 > lighting simple > set bgColor white > graphics silhouettes true > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > lighting flat > lighting simple > volume #2 level 0.1463 > volume #2 level 0.1738 > close session > open /Users/haoyangli/Downloads/cryosparc_P34_J338_004_volume_map.mrc Opened cryosparc_P34_J338_004_volume_map.mrc, grid size 256,256,256, pixel 1.7, shown at level 0.0334, step 1, values float32 > volume #1 level 0.1693 > vop flip #1 axis Z > open ""/Users/haoyangli/Google > Drive/Phenix/20210626_LASV_LIV_FL_372DscFv_89FscFv_27A/RealSpaceRefine_37/GP_89F_035_real_space_refined_037.pdb"" > format pdb Chain information for GP_89F_035_real_space_refined_037.pdb #3 --- Chain | Description A B C | No description available H | No description available L | No description available O Q S | No description available P R T | No description available a b c | No description available > select #3 16782 atoms, 17250 bonds, 2086 residues, 1 model selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected atoms"" > volume #2 color #b2b2b287 > ui tool show ""Fit in Map"" Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map cryosparc_P34_J338_004_volume_map.mrc (#1) using 16782 atoms average map value = 0.3944, steps = 144 shifted from previous position = 23.4 rotated from previous position = 29.2 degrees atoms outside contour = 2799, contour level = 0.16929 Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to cryosparc_P34_J338_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.69067126 -0.72237609 0.03385264 384.18231999 -0.65805864 0.60838594 -0.44365006 215.46441868 0.29988673 -0.32869336 -0.89556051 297.38624159 Axis 0.38724200 -0.89615983 0.21665915 Axis point 226.44252262 0.00000000 190.41112465 Rotation angle (degrees) 171.46404372 Shift along axis 20.11242331 > select /H:2-136 1048 atoms, 1077 bonds, 135 residues, 1 model selected > delete atoms sel > delete bonds sel > select /L:2-109 794 atoms, 811 bonds, 108 residues, 1 model selected > delete atoms sel > delete bonds sel > ui mousemode right ""translate selected models"" > select #3 14940 atoms, 15362 bonds, 1843 residues, 1 model selected Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map cryosparc_P34_J338_004_volume_map.mrc (#1) using 14940 atoms average map value = 0.4023, steps = 128 shifted from previous position = 29.5 rotated from previous position = 11.1 degrees atoms outside contour = 2471, contour level = 0.16929 Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to cryosparc_P34_J338_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.69705133 -0.70756218 0.11608274 375.00662146 -0.62124709 0.51514232 -0.59049170 238.64293114 0.35801046 -0.48371909 -0.79865158 304.49585974 Axis 0.38383654 -0.86970526 0.31029386 Axis point 228.31622372 0.00000000 209.40965166 Rotation angle (degrees) 172.00503731 Shift along axis 30.87542576 > ui mousemode right ""rotate selected models"" Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map cryosparc_P34_J338_004_volume_map.mrc (#1) using 14940 atoms average map value = 0.405, steps = 268 shifted from previous position = 30.7 rotated from previous position = 44.3 degrees atoms outside contour = 2480, contour level = 0.16929 Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to cryosparc_P34_J338_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.49913481 -0.33264473 -0.80013245 369.11913823 -0.80043264 0.53069610 0.27869203 189.56109972 0.33192173 0.77955701 -0.53114859 98.81139685 Axis 0.37848450 -0.85545001 -0.35348942 Axis point 209.13813889 0.00000000 96.62329565 Rotation angle (degrees) 138.57250641 Shift along axis -57.38295523 > ui mousemode right ""translate selected models"" > volume #1 level 0.1365 > close #1 > volume #2 level 0.04382 Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map cryosparc_P34_J338_004_volume_map.mrc z flip (#2) using 14940 atoms average map value = 0.5177, steps = 96 shifted from previous position = 2.41 rotated from previous position = 12.3 degrees atoms outside contour = 14, contour level = 0.043823 Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to cryosparc_P34_J338_004_volume_map.mrc z flip (#2) coordinates: Matrix rotation and translation -0.70237571 -0.68484180 0.19406202 366.27148750 -0.71159044 0.68227881 -0.16773392 191.62360549 -0.01753320 -0.25590491 -0.96654294 341.83502139 Axis -0.38204662 0.91684624 -0.11590235 Axis point 233.83781508 0.00000000 171.51284623 Rotation angle (degrees) 173.37370831 Shift along axis -3.86288335 > volume #2 level 0.1371 Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map cryosparc_P34_J338_004_volume_map.mrc z flip (#2) using 14940 atoms average map value = 0.5177, steps = 40 shifted from previous position = 0.0312 rotated from previous position = 0.00331 degrees atoms outside contour = 77, contour level = 0.13712 Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to cryosparc_P34_J338_004_volume_map.mrc z flip (#2) coordinates: Matrix rotation and translation -0.70241137 -0.68480229 0.19407241 366.25922596 -0.71155455 0.68231861 -0.16772431 191.61265797 -0.01756122 -0.25590456 -0.96654253 341.86731742 Axis -0.38202193 0.91685703 -0.11589839 Axis point 233.82910121 0.00000000 171.52625749 Rotation angle (degrees) 173.37257867 Shift along axis -3.85951704 Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map cryosparc_P34_J338_004_volume_map.mrc z flip (#2) using 14940 atoms average map value = 0.5177, steps = 44 shifted from previous position = 0.00948 rotated from previous position = 0.017 degrees atoms outside contour = 77, contour level = 0.13712 Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to cryosparc_P34_J338_004_volume_map.mrc z flip (#2) coordinates: Matrix rotation and translation -0.70233399 -0.68495040 0.19382961 366.28538947 -0.71163610 0.68223226 -0.16772959 191.63622780 -0.01735036 -0.25573834 -0.96659033 341.82242339 Axis -0.38208865 0.91683464 -0.11585554 Axis point 233.83090473 0.00000000 171.52456066 Rotation angle (degrees) 173.38668645 Shift along axis -3.85677781 > sequence chain #3/A#3/B#3/C Alignment identifier is 1 > color sel cornflower blue > sequence chain #3/a#3/b#3/c Alignment identifier is 2 > color sel hot pink > color sel cornflower blue > color sel hot pink > color zone #2 near #1 distance 12 > color zone #3 near #2 distance 12 > color zone #2 near #3 distance 12 > select ::name=""BMA""::name=""FUC""::name=""MAN""::name=""NAG"" 1062 atoms, 1111 bonds, 82 residues, 1 model selected > color sel cornflower blue > sequence chain #3/a#3/b#3/c Alignment identifier is 1 > color sel cornflower blue > sequence chain #3/O#3/Q#3/S Alignment identifier is 2 > color sel orange > sequence chain #3/P#3/R#3/T Alignment identifier is 3 > color sel orange > color zone #2 near #3 distance 12 > color zone #2 near #3 distance 15 > color zone #2 near #3 distance 10 > color zone #2 near #3 distance 13 > hide #3 models > select #3 14940 atoms, 15362 bonds, 1843 residues, 1 model selected > ~select #3 Nothing selected > volume #2 level 0.3115 > color zone #2 near #3 distance 12 > color zone #2 near #3 distance 10 > volume #2 level 0.35 > lighting soft > graphics silhouettes false > vop gaussian #2 sdev 5.1 > color zone #1 near #3 distance 10 > volume #1 level 0.2347 > color zone #1 near #3 distance 12 > color zone #1 near #3 distance 12 > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSEM.cxs"" includeMaps true opened ChimeraX session > show #!2 models > hide #!1 models > color zone #2 near #3 distance 10 > color zone #2 near #3 distance 12 > color zone #2 near #3 distance 15 > color zone #2 near #3 distance 13 > volume #2 level 0.2514 > color zone #2 near #3 distance 15 > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSEM.cxs"" includeMaps true opened ChimeraX session > close #1-2 > show #3 models > ui tool show ""Show Sequence Viewer"" > sequence chain /O /Q /S Alignment identifier is 1 > sequence chain /P /R /T Alignment identifier is 2 > delete atoms sel > delete bonds sel > delete atoms sel > delete bonds sel > save > /Users/haoyang/Google_Drive_LJI/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/CysRRLL_INOG_WT_NSEM.cxs > open > /Users/haoyang/Google_Drive_LJI/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc Opened WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc, grid size 256,256,256, pixel 1.7, shown at level 0.0376, step 1, values float32 > volume #1 level 0.2164 > volume #1 color #b2b2b2fb > volume #1 color #b2b2b2e9 > volume #1 color #b2b2b2bd > volume #1 color #b2b2b274 > volume #1 color #b2b2b271 > volume #1 color #b2b2b26f > volume #1 color #b2b2b26e > volume #1 color #b2b2b26d > volume #1 color #b2b2b26c > volume #1 color #b2b2b26b > volume #1 color #b2b2b26a > volume #1 color #b2b2b268 > volume #1 color #b2b2b267 > volume #1 color #b2b2b262 > volume #1 color #b2b2b260 > volume #1 color #b2b2b261 > volume #1 color #b2b2b263 > volume #1 color #b2b2b265 > volume #1 color #b2b2b26b > volume #1 color #b2b2b271 > volume #1 color #b2b2b276 > volume #1 color #b2b2b277 > volume #1 color #b2b2b278 > volume #1 color #b2b2b27d > volume #1 color #b2b2b281 > volume #1 color #b2b2b284 > volume #1 color #b2b2b285 > volume #1 color #b2b2b287 > volume #1 color #b2b2b289 > volume #1 color #b2b2b28a > volume #1 color #b2b2b28b > volume #1 color #b2b2b28d > volume #1 color #b2b2b28f > volume #1 color #b2b2b294 > volume #1 color #b2b2b297 > volume #1 color #b2b2b29d > volume #1 color #b2b2b2a1 > volume #1 color #b2b2b2a4 > select #3 9645 atoms, 9932 bonds, 1156 residues, 1 model selected > select #1 2 models selected > select #3 9645 atoms, 9932 bonds, 1156 residues, 1 model selected > select #1 2 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui tool show ""Fit in Map"" Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc (#1) using 9645 atoms average map value = 0.5301, steps = 168 shifted from previous position = 14.6 rotated from previous position = 48.8 degrees atoms outside contour = 762, contour level = 0.21641 Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc (#1) coordinates: Matrix rotation and translation -0.98048923 -0.17332729 -0.09272815 336.81000333 0.18581598 -0.97114052 -0.14952759 356.22342895 -0.06413485 -0.16384056 0.98439981 166.19874474 Axis -0.03969608 -0.07930160 0.99605998 Axis point 155.01660267 200.31825196 0.00000000 Rotation angle (degrees) 169.61381710 Shift along axis 123.92479216 > ui mousemode right ""rotate selected models"" > vop flip #1 axis Z > select #2 2 models selected > ui mousemode right ""translate selected models"" Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip (#2) using 9645 atoms average map value = 0.5452, steps = 160 shifted from previous position = 7.36 rotated from previous position = 40.4 degrees atoms outside contour = 660, contour level = 0.21641 Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip (#2) coordinates: Matrix rotation and translation 0.64139211 0.75631872 -0.12883376 56.87855910 0.70209586 -0.64632118 -0.29888178 274.34396971 -0.30931788 0.10124677 -0.94555356 307.42004625 Axis 0.90468148 0.40807045 -0.12259665 Axis point 0.00000000 104.36813840 171.36502302 Rotation angle (degrees) 167.22380457 Shift along axis 125.71997824 Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip (#2) using 9645 atoms average map value = 0.5452, steps = 44 shifted from previous position = 0.00164 rotated from previous position = 0.00431 degrees atoms outside contour = 660, contour level = 0.21641 Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip (#2) coordinates: Matrix rotation and translation 0.64137799 0.75631940 -0.12890010 56.88582627 0.70207968 -0.64632504 -0.29891144 274.34784440 -0.30938388 0.10121708 -0.94553514 307.42941901 Axis 0.90467751 0.40806794 -0.12263423 Axis point 0.00000000 104.36745270 171.37191875 Rotation angle (degrees) 167.22374860 Shift along axis 125.71451854 > ~select #2 Nothing selected > volume #1 color #b2b2b2a5 > volume #1 color #b2b2b2af > volume #1 color #b2b2b2bf > volume #1 color #b2b2b2d2 > volume #1 color #b2b2b2eb > volume #1 color #b2b2b2 > select #2 2 models selected > volume #2 color #b2b2b2a6 > volume #2 color #b2b2b2ad > volume #2 color #b2b2b2c0 > volume #2 color #b2b2b2dc > volume #2 color #b2b2b2fd > volume #2 color #b2b2b2 > color zone #2 near #3 distance 10 > color zone #2 near #3 distance 15 > color zone #2 near #3 distance 13 > color zone #2 near #3 distance 15 > hide #3 models > select clear > vop gaussian #2 sdev 5.1 > volume #4 level 0.1778 > volume #4 color #b3b3b3 > color zone #4 near #3 distance 15 > color zone #4 near #3 distance 13 > color zone #4 near #3 distance 10 > color zone #4 near #3 distance 12 > color zone #4 near #3 distance 13 > volume #4 color #b3b3b3fc > volume #4 color #b3b3b3f5 > volume #4 color #b3b3b3f1 > volume #4 color #b3b3b3e6 > volume #4 color #b3b3b3e0 > volume #4 color #b3b3b3da > volume #4 color #b3b3b3d6 > volume #4 color #b3b3b3d5 > volume #4 color #b3b3b3d2 > volume #4 color #b3b3b3ce > volume #4 color #b3b3b3c7 > volume #4 color #b3b3b3c2 > volume #4 color #b3b3b3bc > volume #4 color #b3b3b3b9 > volume #4 color #b3b3b3b8 > volume #4 color #b3b3b3b7 > volume #4 color #b3b3b3ac > volume #4 color #b3b3b3a5 > volume #4 color #b3b3b3a1 > volume #4 color #b3b3b3a0 > show #3 models > select #3 9645 atoms, 9932 bonds, 1156 residues, 1 model selected > volume #4 color #b3b3b3a1 > volume #4 color #b3b3b3a3 > volume #4 color #b3b3b3a9 > volume #4 color #b3b3b3b4 > volume #4 color #b3b3b3bd > volume #4 color #b3b3b3d1 > volume #4 color #b3b3b3e4 > volume #4 color #b3b3b3f5 > volume #4 color #b3b3b3 > color zone #4 near #3 distance 13 > hide #3 models > ~select #3 Nothing selected > show #3 models > volume #4 color #b3b3b3fe > volume #4 color #b3b3b3f8 > volume #4 color #b3b3b3ef > volume #4 color #b3b3b3e6 > volume #4 color #b3b3b3dd > volume #4 color #b3b3b3cc > volume #4 color #b3b3b3c4 > volume #4 color #b3b3b3bf > volume #4 color #b3b3b3b8 > volume #4 color #b3b3b3b4 > volume #4 color #b3b3b3b1 > volume #4 color #b3b3b3ab > volume #4 color #b3b3b3a7 > volume #4 color #b3b3b3a6 > volume #4 color #b3b3b3a4 > volume #4 color #b3b3b3a2 > volume #4 color #b3b3b39e > color zone #4 near #3 distance 15 > select #3 9645 atoms, 9932 bonds, 1156 residues, 1 model selected > color zone #4 near #3 distance 15 > hide #3 models > color zone #4 near #3 distance 13 > color zone #4 near #3 distance 14 > color zone #4 near #3 distance 15 > volume #4 color #b3b3b3a8 > volume #4 color #b3b3b3be > volume #4 color #b3b3b3d9 > volume #4 color #b3b3b3 > color zone #4 near #3 distance 15 > save > /Users/haoyang/Google_Drive_LJI/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/CysRRLL_INOG_WT_NSEM.cxs > includeMaps true opened ChimeraX session > show #3 models > hide #3 models > show #3 models > hide #3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_377H.cxs"" > close #1-2 > show #3 models > hide #!4 models > show #!4 models > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_377H.cxs"" > open ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/5vk2_377H.pdb"" 5vk2_377H.pdb title: Structural basis for antibody-mediated neutralization of lassa virus [more info...] Chain information for 5vk2_377H.pdb #1 --- Chain | Description A B C | pre-glycoprotein polyprotein GP complex D F H | fab 37.7H heavy chain E G L | fab 37.7H light chain a b c | pre-glycoprotein polyprotein GP complex Non-standard residues in 5vk2_377H.pdb #1 --- BMA — β-D-mannopyranose FUC — α-L-fucopyranose MAN — α-D-mannopyranose NAG — 2-acetamido-2-deoxy-β-D-glucopyranose > mmaker #1/A to #3/A showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker GP_89F_035_real_space_refined_037.pdb, chain A (#3) with 5vk2_377H.pdb, chain A (#1), sequence alignment score = 1006.2 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 5vk2_377H.pdb #1/A, GP_89F_035_real_space_refined_037.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 180 pruned atom pairs is 0.540 angstroms; (across all 186 pairs: 0.910) > select #4 2 models selected > select #3 9645 atoms, 9932 bonds, 1156 residues, 1 model selected > open ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc"" Opened WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc, grid size 256,256,256, pixel 1.7, shown at level 0.127, step 1, values float32 > select #2 2 models selected > hide #!4 models > hide #3 models > ui mousemode right ""rotate selected models"" > ui tool show ""Fit in Map"" Fit map WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc in map WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian using 167760 points correlation = 0.663, correlation about mean = 0.2592, overlap = 1.605e+04 steps = 160, shift = 29.6, angle = 15.3 degrees Position of WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc (#2) relative to WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian (#4) coordinates: Matrix rotation and translation 0.70576768 -0.70799007 -0.02533847 223.08775843 -0.70843650 -0.70515209 -0.02963510 531.45132478 0.00311388 0.03886619 -0.99923957 421.83274303 Axis 0.92348968 -0.38357605 -0.00601857 Axis point 0.00000000 307.81922727 216.97963673 Rotation angle (degrees) 177.87451049 Shift along axis -0.37159010 > show #3 models > hide #3 models > show #!4 models > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > volume #4 level 0.1812 > volume #2 level 0.2904 > volume #2 color #b3b3b387 > vop flip #2 axis Z > hide #!4 models > select #4 2 models selected > ~select #4 Nothing selected > select #5 2 models selected > vop gaussian #5 sdev 5.1 > select #6 2 models selected > ui mousemode right ""translate selected models"" Fit molecule 5vk2_377H.pdb (#1) to map WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip gaussian (#6) using 18672 atoms average map value = 0.4481, steps = 136 shifted from previous position = 22.8 rotated from previous position = 21.5 degrees atoms outside contour = 618, contour level = 0.12427 Position of 5vk2_377H.pdb (#1) relative to WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip gaussian (#6) coordinates: Matrix rotation and translation -0.46173942 -0.88060213 -0.10647345 226.76312435 -0.88456595 0.46604971 -0.01845904 132.15488486 0.06587699 0.08565952 -0.99414418 233.97249263 Axis 0.51697972 -0.85577135 -0.01968158 Axis point 146.39941073 -0.00000000 122.16150024 Rotation angle (degrees) 174.22058307 Shift along axis -0.46737797 > show #!5 models Fit map WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip in map WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip gaussian using 117889 points correlation = 0.9917, correlation about mean = 0.8723, overlap = 2.621e+04 steps = 180, shift = 20.5, angle = 29.4 degrees Position of WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip (#5) relative to WT_CysRRLL_srtA_INOG_377HFab_P34_J433.mrc z flip gaussian (#6) coordinates: Matrix rotation and translation 0.99999944 0.00105727 0.00007889 -0.23280697 -0.00105715 0.99999820 -0.00157322 0.56981858 -0.00008055 0.00157314 0.99999876 -0.09383230 Axis 0.82926089 0.04202061 -0.55727969 Axis point 0.00000000 101.31860533 365.20261645 Rotation angle (degrees) 0.10869527 Shift along axis -0.11682275 > ~select #6 Nothing selected > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > hide #!6 models > volume #5 level 0.1854 > close #6 > color zone #5 near #2 distance 12 > color zone #5 near #1 distance 12 > volume #5 level 0.2935 > color zone #5 near #1 distance 12 > volume #5 level 0.2661 > color zone #5 near #1 distance 15 > sequence chain #1/D#1/F#1/H Alignment identifier is 1 > color sel orange red > select #1/E#1/G#1/L 4749 atoms, 4875 bonds, 634 residues, 1 model selected > color sel orange red > color zone #5 near #1 distance 15 > color zone #5 near #1 distance 14 > hide #!1 models > color zone #5 near #1 distance 12 > volume #5 level 0.3828 > color zone #5 near #1 distance 13 > color zone #5 near #1 distance 13 > volume #5 level 0.35 > volume #5 level 0.3 > color zone #5 near #1 distance 15 > volume #5 level 0.25 > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_377H.cxs"" > includeMaps true > color zone #5 near #1 distance 16 > save /Users/haoyangli/Desktop/image5.png supersample 3 > color zone #5 near #1 distance 16 > color zone #5 near #1 distance 14 > color zone #5 near #1 distance 15 > save /Users/haoyangli/Desktop/image6.png supersample 3 > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_377H.cxs"" > includeMaps true > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_197E.cxs"" > includeMaps true > close #1-2,5 > open ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc"" Opened WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc, grid size 256,256,256, pixel 1.7, shown at level 0.138, step 1, values float32 > show #3 models > ui tool show ""Fit in Map"" Fit map WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc in map WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian using 167722 points correlation = 0.6062, correlation about mean = 0.4046, overlap = 1.116e+04 steps = 808, shift = 45.9, angle = 84.1 degrees Position of WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) relative to WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian (#4) coordinates: Matrix rotation and translation -0.99021450 -0.13955195 -0.00069218 462.65938569 0.13953390 -0.99014554 0.01192009 397.56536334 -0.00234883 0.01170687 0.99992871 -51.44987377 Axis -0.00076400 0.00593589 0.99998209 Axis point 217.36170723 215.15420106 0.00000000 Rotation angle (degrees) 171.97845737 Shift along axis -49.44251938 > show #!4 models > volume #1 level 0.1842 > ui mousemode right ""rotate selected models"" > select #1 2 models selected Fit map WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc in map WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian using 147086 points correlation = 0.6461, correlation about mean = 0.2283, overlap = 1.379e+04 steps = 416, shift = 30.3, angle = 44.2 degrees Position of WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) relative to WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian (#4) coordinates: Matrix rotation and translation 0.55459277 0.83209463 -0.00673578 -82.77771676 0.83039376 -0.55394428 -0.05993266 171.68729837 -0.05360089 0.02764487 -0.99817969 439.90905021 Axis 0.88156614 0.47174993 -0.01712122 Axis point 0.00000000 101.79137113 221.56736430 Rotation angle (degrees) 177.15285770 Shift along axis 0.48766077 > volume #1 color #999999 > volume #1 color #b3b3b3 > volume #1 level 0.2 > volume #1 color #b3b3b37f > volume #1 color #b3b3b380 > hide #!4 models > open ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/12.1F_Fab.pdb"" Chain information for 12.1F_Fab.pdb #2 --- Chain | Description H | No description available L | No description available > select #2 3344 atoms, 3296 bonds, 2 pseudobonds, 546 residues, 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" Fit molecule GP_89F_035_real_space_refined_037.pdb (#3) to map WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) using 9645 atoms average map value = 0.3369, steps = 84 shifted from previous position = 2.79 rotated from previous position = 12.1 degrees atoms outside contour = 1593, contour level = 0.2 Position of GP_89F_035_real_space_refined_037.pdb (#3) relative to WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) coordinates: Matrix rotation and translation 0.99011269 -0.12634234 -0.06094662 154.13611387 0.12777199 0.99159897 0.02014451 56.71830280 0.05788950 -0.02773261 0.99793773 131.98613278 Axis -0.16823518 -0.41757764 0.89293104 Axis point -577.75617756 1356.06792412 0.00000000 Rotation angle (degrees) 8.18051056 Shift along axis 68.23910360 Fit molecule 12.1F_Fab.pdb (#2) to map WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) using 3344 atoms average map value = 0.4006, steps = 200 shifted from previous position = 46.4 rotated from previous position = 13.9 degrees atoms outside contour = 325, contour level = 0.2 Position of 12.1F_Fab.pdb (#2) relative to WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) coordinates: Matrix rotation and translation -0.82175967 0.43583550 -0.36709466 -28.04937749 0.12218975 0.76400188 0.63353833 440.21967352 0.55657950 0.47576104 -0.68108055 -66.50171599 Axis -0.15966930 -0.93475055 -0.31740689 Axis point -24.90473847 0.00000000 -120.66840638 Rotation angle (degrees) 150.39121272 Shift along axis -385.90885256 > open ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/12.1F_Fab.pdb"" Chain information for 12.1F_Fab.pdb #5 --- Chain | Description H | No description available L | No description available > select #5 3344 atoms, 3296 bonds, 2 pseudobonds, 546 residues, 2 models selected > ui mousemode right ""translate selected models"" Fit molecule 12.1F_Fab.pdb (#5) to map WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) using 3344 atoms average map value = 0.4019, steps = 304 shifted from previous position = 22.3 rotated from previous position = 108 degrees atoms outside contour = 162, contour level = 0.2 Position of 12.1F_Fab.pdb (#5) relative to WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) coordinates: Matrix rotation and translation -0.77732189 -0.37326612 -0.50640209 25.97470394 0.03377099 0.77903999 -0.62606407 -8.51748442 0.62819599 -0.50375501 -0.59295927 5.69004618 Axis 0.10094918 -0.93645344 0.33595271 Axis point 12.26034921 0.00000000 5.76863493 Rotation angle (degrees) 142.71391108 Shift along axis 12.50993905 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" Fit molecule 12.1F_Fab.pdb (#5) to map WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) using 3344 atoms average map value = 0.3904, steps = 100 shifted from previous position = 20.8 rotated from previous position = 14.5 degrees atoms outside contour = 289, contour level = 0.2 Position of 12.1F_Fab.pdb (#5) relative to WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) coordinates: Matrix rotation and translation 0.41107464 -0.82451862 -0.38882735 153.38537500 0.85318879 0.19775456 0.48266142 476.67588214 -0.32107094 -0.53015300 0.78476192 471.27459800 Axis -0.51650775 -0.03455392 0.85558505 Axis point -128.67321405 470.57837099 0.00000000 Rotation angle (degrees) 78.65036600 Shift along axis 307.51974417 > open ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/12.1F_Fab.pdb"" Chain information for 12.1F_Fab.pdb #6 --- Chain | Description H | No description available L | No description available > select #6 3344 atoms, 3296 bonds, 2 pseudobonds, 546 residues, 2 models selected Fit molecule 12.1F_Fab.pdb (#6) to map WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) using 3344 atoms average map value = 0.4068, steps = 204 shifted from previous position = 22.5 rotated from previous position = 82.8 degrees atoms outside contour = 320, contour level = 0.2 Position of 12.1F_Fab.pdb (#6) relative to WT_CysRRLL_srtA_INOG_197EFab_P34_J419.mrc (#1) coordinates: Matrix rotation and translation 0.30197533 -0.84840729 -0.43475967 120.13084230 -0.78237386 0.04002208 -0.62152183 -102.52211603 0.54470363 0.52782886 -0.65168601 -57.53517381 Axis 0.76039013 -0.64799563 0.04368655 Axis point 0.00000000 19.24108198 -32.79209306 Rotation angle (degrees) 130.90784484 Shift along axis 155.26667653 > color zone #1 near #2 #3 #5 #6 distance 15 > color zone #1 near #2 #3 #5 #6 distance 15 > hide #!2 models > hide #3 models > hide #!5 models > hide #!6 models > ~select #6 Nothing selected > save /Users/haoyangli/Desktop/image7.png supersample 3 > save /Users/haoyangli/Desktop/image8.png supersample 3 > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_197E.cxs"" > includeMaps true > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_197E.cxs"" > includeMaps true > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_2510C.cxs"" > includeMaps true > close #1 > close #5 > close #6 > close #2 > open ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc"" Opened WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc, grid size 256,256,256, pixel 1.7, shown at level 0.0969, step 1, values float32 > open ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/2510C-LIV-LASV-12bGP.pdb"" Summary of feedback from opening /Users/haoyangli/Google Drive/LASVGP_Arevirumab/EMmaps/CysRRLL_INOG_NSmaps/2510C-LIV-LASV-12bGP.pdb --- warnings | Start residue of secondary structure not found: HELIX 46 46 ASN 1 162 GLY 1 164 5 3 Start residue of secondary structure not found: HELIX 47 47 SER 1 193 GLY 1 197 5 5 Start residue of secondary structure not found: HELIX 48 48 ASN 2 162 GLY 2 164 5 3 Start residue of secondary structure not found: HELIX 49 49 SER 2 193 GLY 2 197 5 5 Start residue of secondary structure not found: HELIX 50 50 ASN 3 162 GLY 3 164 5 3 22 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (147 ) Cannot find LINK/SSBOND residue CYS (147 ) Cannot find LINK/SSBOND residue CYS (147 ) Chain information for 2510C-LIV-LASV-12bGP.pdb #2 --- Chain | Description A B C | No description available D G J | No description available E H K | No description available > volume #1 level 0.3562 Fit map WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc in map WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian using 106123 points correlation = 0.6784, correlation about mean = -0.01018, overlap = 1.732e+04 steps = 408, shift = 30.3, angle = 66 degrees Position of WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc (#1) relative to WT_CysRRLL_srtA_INOG_P34_J339_17A.mrc z flip gaussian (#4) coordinates: Matrix rotation and translation -0.90718349 -0.16565403 -0.38675167 538.56945391 -0.39854732 0.04377414 0.91610253 100.12591732 -0.13482636 0.98521193 -0.10573215 64.46373715 Axis 0.19747014 -0.71984021 -0.66545895 Axis point 279.42151287 -0.00000000 19.04011409 Rotation angle (degrees) 169.92210037 Shift along axis -8.62124657 > show #!4 models > close #3 > close #4 > select #1 2 models selected > ~select #1 Nothing selected > select #2 17148 atoms, 17550 bonds, 42 pseudobonds, 2166 residues, 2 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" Fit molecule 2510C-LIV-LASV-12bGP.pdb (#2) to map WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc (#1) using 17148 atoms average map value = 0.5426, steps = 180 shifted from previous position = 42 rotated from previous position = 24.8 degrees atoms outside contour = 3712, contour level = 0.35616 Position of 2510C-LIV-LASV-12bGP.pdb (#2) relative to WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc (#1) coordinates: Matrix rotation and translation 0.79560198 0.60581577 0.00217737 -32.12655918 -0.60579072 0.79559395 -0.00691809 184.60555379 -0.00592339 0.00418501 0.99997370 44.28889132 Axis 0.00916336 0.00668553 -0.99993567 Axis point 258.15211222 139.47332906 0.00000000 Rotation angle (degrees) 37.28947192 Shift along axis -43.34624320 > select up 17148 atoms, 17550 bonds, 42 pseudobonds, 2166 residues, 2 models selected > ~select #2 Nothing selected > select #2 17148 atoms, 17550 bonds, 42 pseudobonds, 2166 residues, 2 models selected > vop flip #1 axis Z > select #3 2 models selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" Fit molecule 2510C-LIV-LASV-12bGP.pdb (#2) to map WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc z flip (#3) using 17148 atoms average map value = 0.6296, steps = 160 shifted from previous position = 8.65 rotated from previous position = 24.7 degrees atoms outside contour = 1632, contour level = 0.35616 Position of 2510C-LIV-LASV-12bGP.pdb (#2) relative to WT_CysRRLL_srtA_INOG_2510CFab_P34_J420.mrc z flip (#3) coordinates: Matrix rotation and translation 0.99422172 0.10732870 0.00193569 21.66191515 0.10733834 -0.99420526 -0.00586441 376.14651114 0.00129506 0.00603830 -0.99998094 387.14059424 Axis 0.99855439 0.05374452 0.00080883 Axis point 0.00000000 186.91268192 194.11941524 Rotation angle (degrees) 179.65851662 Shift along axis 42.15954571 > sequence chain #2/D#2/G#2/J Alignment identifier is 1 > color sel #808003ff > sequence chain #2/E#2/H#2/K Alignment identifier is 2 > color sel #408002ff > color sel #808003ff > color zone #3 near #2 distance 15 > hide #!2 models > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_2510C.cxs"" > includeMaps true > save /Users/haoyangli/Desktop/image9.png supersample 3 > save /Users/haoyangli/Desktop/image10.png supersample 3 > save ""/Users/haoyangli/Google > Drive/LASVGP_Arevirumab/EMmaps/NativeGP_April15_2022_glycans_2510C.cxs"" > includeMaps true opened ChimeraX session OpenGL version: 4.1 ATI-4.2.15 OpenGL renderer: AMD Radeon Pro 575 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac18,3 Processor Name: Quad-Core Intel Core i5 Processor Speed: 3.5 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Memory: 32 GB System Firmware Version: 429.80.1.0.0 SMC Version (system): 2.41f2 Software: System Software Overview: System Version: macOS 11.2.3 (20D91) Kernel Version: Darwin 20.3.0 Time since boot: 5 days 6:03 Graphics/Displays: Radeon Pro 575: Chipset Model: Radeon Pro 575 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c4 ROM Revision: 113-D000AA-931 VBIOS Version: 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