id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6481 Crash closing tool chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4.dev202203230115 (2022-03-23 01:15:14 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003261a0000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1284 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000324f91000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000323f8e000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000322f8b000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000321f88000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000320f85000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031ff82000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031ef7f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031df7c000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031cf79000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031bf76000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031af73000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000319f70000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000000318f6d000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00000002049b6600 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 2309 in destroy File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 2177 in _destroy File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 807 in remove_tool File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 370 in remove_tool File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py"", line 154 in delete File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/seq-view/tool.py"", line 510 in delete File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 674 in close_request File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 2275 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 318 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2022-03-28 17:05:03.00 -0400"",""app_version"":""1.4.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.4.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.3 (21E230)"",""incident_id"":""39AF051D-2BD8-4E8A-BFBA-BD7AD8A1D6B2"",""name"":""ChimeraX""} { ""uptime"" : 39000, ""procLaunch"" : ""2022-03-28 16:42:17.4019 -0400"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,3"", ""procStartAbsTime"" : 909428520771, ""coalitionID"" : 2964, ""osVersion"" : { ""train"" : ""macOS 12.3"", ""build"" : ""21E230"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2022-03-28 17:05:02.7571 -0400"", ""incident"" : ""39AF051D-2BD8-4E8A-BFBA-BD7AD8A1D6B2"", ""bug_type"" : ""309"", ""pid"" : 9385, ""procExitAbsTime"" : 938872935466, ""translated"" : true, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.4.0"",""CFBundleVersion"":""1.4.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""4B6B6653-3946-5597-9ADC-6337C89A37EC"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""27F788B4-918C-4291-0279-F12BB565DCE2"", ""wakeTime"" : 710, ""sleepWakeUUID"" : ""74FAA04B-E5DB-4C6E-84E9-B324C3C1D678"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x46958b8617c8 is not in any region. Bytes after previous region: 77127068555209 Bytes before following region: 27945011374136\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-6000012d6000 [ 18.8M] rw-\/rwx SM=ZER "", ""isCorpse"" : 1, ""exception"" : {""codes"":""0x0000000000000001, 0x000046958b8617c8"",""rawCodes"":[1,77608104892360],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x000046958b8617c8""}, ""vmregioninfo"" : ""0x46958b8617c8 is not in any region. 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""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 3520K 4 \nCG image 1484K 65 \nColorSync 244K 29 \nCoreAnimation 5096K 88 \nCoreGraphics 12K 2 \nCoreUI image data 5168K 39 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.3G 306 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 1.0G 10 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1492K 370 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 1220K 122 \nRosetta Thread Context 1220K 122 \nSTACK GUARD 76K 19 \nStack 383.4M 62 \nStack Guard 56.2M 43 \nVM_ALLOCATE 135.6M 268 \nVM_ALLOCATE (reserved) 192.0M 6 reserved VM address space (unallocated)\n__DATA 44.8M 652 \n__DATA_CONST 31.0M 346 \n__DATA_DIRTY 1666K 219 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 738.9M 126 \n__OBJC_RO 82.6M 1 \n__OBJC_RW 3200K 2 \n__TEXT 779.9M 652 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 5.3G 1091 \nshared memory 3152K 27 \nunshared pmap 12.2M 9 \n=========== ======= ======= \nTOTAL 10.3G 4716 \nTOTAL, minus reserved VM space 9.0G 4716 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000123 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.4.dev202203230115 (2022-03-23) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/haobowang/Desktop/4qyz_Cse1_colored.pdb format pdb 4qyz_Cse1_colored.pdb title: Crystal structure of A crispr RNA-guided surveillance complex, cascade, bound to A ssDNA target [more info...] Chain information for 4qyz_Cse1_colored.pdb #1 --- Chain | Description | UniProt A | crispr system cascade subunit casa | CSE1_ECOLI B C | crispr system cascade subunit casb | CSE2_ECOLI D | crispr system cascade subunit casc | CASC_ECOLI E | crispr system cascade subunit casc | CASC_ECOLI F | crispr system cascade subunit casc | CASC_ECOLI G | crispr system cascade subunit casc | CASC_ECOLI H | crispr system cascade subunit casc | CASC_ECOLI I | crispr system cascade subunit casc | CASC_ECOLI J | crispr system cascade subunit casd | CAS5_ECOLI K | crispr system cascade subunit case | CAS6_ECOLI L | RNA (55-mer) | M | DNA (33-mer) | Non-standard residues in 4qyz_Cse1_colored.pdb #1 --- ZN — zinc ion > ui mousemode right ""translate selected models"" > ui mousemode right zoom > open /Users/haobowang/Downloads/5h9e.pdb 5h9e.pdb title: Crystal structure of E. Coli cascade bound to A pam-containing dsDNA target (32-NT spacer) At 3.20 angstrom resolution. [more info...] Chain information for 5h9e.pdb #2 --- Chain | Description | UniProt A | crispr system cascade subunit casa | CSE1_ECOLI B | crispr system cascade subunit casb | CSE2_ECOLI C | crispr system cascade subunit casb | CSE2_ECOLI D | crispr system cascade subunit casc | CASC_ECOLI E | crispr system cascade subunit casc | CASC_ECOLI F | crispr system cascade subunit casc | CASC_ECOLI G | crispr system cascade subunit casc | CASC_ECOLI H | crispr system cascade subunit casc | CASC_ECOLI I | crispr system cascade subunit casc | CASC_ECOLI J | crispr system cascade subunit casd | CAS5_ECOLI K | crispr system cascade subunit case | CAS6_ECOLI L | crRNA (61-mer) | M | DNA (47-mer) non-target | N | DNA (47-mer) target | Non-standard residues in 5h9e.pdb #2 --- 23G — guanosine-5'-phosphate-2',3'-cyclic phosphate ZN — zinc ion > select add #2 27217 atoms, 27942 bonds, 26 pseudobonds, 3351 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,5.9943,0,1,0,45.309,0,0,1,136.56 > view matrix models #2,1,0,0,-40.347,0,1,0,140.44,0,0,1,229.84 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.10134,-0.97584,0.19359,-11.197,-0.966,0.049996,-0.25365,140.18,0.23785,-0.21271,-0.94773,107.32 > view matrix models > #2,0.47569,0.083318,0.87566,7.1519,0.11453,0.98116,-0.15557,132.56,-0.87213,0.17429,0.45719,168.74 > view matrix models > #2,0.26795,-0.61831,0.73885,20.225,0.93981,0.33651,-0.059225,179.59,-0.21201,0.71025,0.67126,176.04 > view matrix models > #2,-0.65902,-0.64601,0.38517,-21.152,0.75208,-0.56029,0.34707,238.13,-0.0084027,0.51841,0.85509,199.99 > view matrix models > #2,-0.4025,-0.54841,0.73297,4.236,0.67052,-0.72172,-0.17179,206.66,0.62321,0.42233,0.65822,202.15 > view matrix models > #2,0.061939,-0.96588,0.25149,-4.4057,0.81693,-0.095698,-0.56874,158.23,0.5734,0.24068,0.78313,216.74 > view matrix models > #2,0.033014,-0.9721,0.23221,-6.0657,0.84088,-0.098567,-0.53217,161.34,0.54022,0.21283,0.81417,219.3 > view matrix models > #2,-0.49526,-0.66179,0.56281,-5.0675,0.7993,-0.60092,-0.0032392,216.27,0.34034,0.44825,0.82658,207.39 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.49526,-0.66179,0.56281,3.1907,0.7993,-0.60092,-0.0032392,216.32,0.34034,0.44825,0.82658,234.63 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.57719,-0.69702,0.42546,-6.5872,0.81045,-0.55284,0.19377,228.39,0.10015,0.45666,0.88399,233.66 > view matrix models > #2,-0.12399,-0.59758,0.79217,23.838,0.52208,-0.71818,-0.46005,183.71,0.84384,0.35653,0.40103,218.28 > view matrix models > #2,-0.58159,-0.71353,-0.39067,-62.685,0.57809,-0.7004,0.41863,245.1,-0.57233,0.017629,0.81983,232.87 > view matrix models > #2,-0.54961,0.78101,-0.29657,-112.15,-0.45142,-0.57634,-0.68121,144.21,-0.70296,-0.24052,0.66933,229.68 > view matrix models > #2,-0.152,0.80504,-0.57341,-124.6,-0.71732,-0.48897,-0.49634,148.6,-0.67996,0.33587,0.6518,207.08 > view matrix models > #2,0.60786,0.50932,0.60918,-16.669,0.31772,0.5471,-0.77443,110.03,-0.72771,0.66429,0.17074,160.33 > view matrix models > #2,0.028532,-0.15975,0.98675,23.7,0.99874,-0.036135,-0.034729,196.59,0.041204,0.9865,0.15851,162.11 > view matrix models > #2,-0.052341,-0.22267,0.97349,23.603,0.98318,-0.1823,0.011165,205.01,0.17498,0.9577,0.22847,170.64 > view matrix models > #2,-0.053257,-0.22508,0.97288,23.635,0.98346,-0.18071,0.012029,205.02,0.1731,0.95744,0.23099,170.78 > view matrix models > #2,-0.12575,-0.50447,0.85422,24.584,0.98997,-0.007875,0.14109,207.55,-0.064447,0.86339,0.5004,188.46 > view matrix models > #2,-0.14687,-0.61172,0.77732,22.902,0.97824,-0.20624,0.02253,206.61,0.14653,0.76372,0.6287,205.21 > select subtract #2 Nothing selected > ui mousemode right zoom > ui mousemode right ""translate selected models"" > ui mousemode right zoom > ui mousemode right ""rotate selected models"" > select add #2 27217 atoms, 27942 bonds, 26 pseudobonds, 3351 residues, 3 models selected > view matrix models > #2,-0.21245,-0.60288,0.76902,20.726,0.97118,-0.21731,0.097931,212.13,0.10808,0.76766,0.63167,204.53 > view matrix models > #2,-0.31191,-0.5842,0.74928,16.73,0.91042,-0.40933,0.059848,215.58,0.27174,0.70083,0.65954,212.15 > view matrix models > #2,-0.44422,-0.7126,0.54301,4.7258,0.88818,-0.42975,0.16263,223.06,0.11746,0.55454,0.82383,226.11 > view matrix models > #2,-0.48388,-0.70095,0.52396,2.1971,0.87065,-0.44609,0.20729,226.44,0.088437,0.55649,0.82614,225.64 > view matrix models > #2,-0.45462,-0.70498,0.54436,4.3299,0.8834,-0.43487,0.1746,223.99,0.11363,0.56027,0.82048,225.59 > view matrix models > #2,-0.42972,-0.5578,0.71007,10.736,0.87477,-0.45215,0.1742,224.45,0.22388,0.696,0.68224,212.98 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.42972,-0.5578,0.71007,17.779,0.87477,-0.45215,0.1742,240.62,0.22388,0.696,0.68224,203.5 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.37005,-0.67924,0.6338,18.237,0.90362,-0.42157,0.075803,233.19,0.2157,0.60076,0.76978,213.02 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.37005,-0.67924,0.6338,24.042,0.90362,-0.42157,0.075803,228.21,0.2157,0.60076,0.76978,222.58 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.33574,-0.7033,0.62661,25.117,0.90907,-0.41616,0.019994,224.24,0.24671,0.57635,0.77907,224.74 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.39292,-0.72217,0.56928,20.75,0.87622,-0.48187,-0.0065206,224.25,0.27903,0.49625,0.82212,231.39 > view matrix models > #2,-0.38263,-0.72267,0.57563,21.408,0.88187,-0.47146,-0.0056973,224.03,0.2755,0.50545,0.81769,230.67 > view matrix models > #2,-0.40977,-0.70076,0.58397,20.633,0.87,-0.49268,0.019266,226.33,0.27421,0.51594,0.81155,229.82 > view matrix models > #2,-0.32266,-0.74648,0.58195,23.905,0.90785,-0.418,-0.032824,220.62,0.26776,0.51773,0.81256,229.7 > select subtract #2 Nothing selected > ui mousemode right ""translate selected models"" > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/C Alignment identifier is 2/C > sequence chain #2/D Alignment identifier is 2/D > sequence chain #2/E Alignment identifier is 2/E > sequence chain #2/F Alignment identifier is 2/F > sequence chain #2/G Alignment identifier is 2/G > sequence chain #2/H Alignment identifier is 2/H > sequence chain #2/I Alignment identifier is 2/I > sequence chain #2/J Alignment identifier is 2/J > sequence chain #2/K Alignment identifier is 2/K > sequence chain #2/L Alignment identifier is 2/L > sequence chain #2/M Alignment identifier is 2/M > sequence chain #2/N Alignment identifier is 2/N > select #2/A:2 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:2-495 3728 atoms, 3811 bonds, 3 pseudobonds, 481 residues, 2 models selected > color (#!2 & sel) #f1ecf3ff > color (#!2 & sel) #2283f3ff > color (#!2 & sel) #1a8cf3ff > select #2/A:2 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:2-225 1680 atoms, 1716 bonds, 1 pseudobond, 220 residues, 2 models selected > select > #2/A:23-29,40-59,63-73,76-91,115-118,124-131,141-154,180-188,191-199,224-233,310-322,328-338,376-406,414-438,442-470,475-492 1860 atoms, 1874 bonds, 235 residues, 1 model selected > select #2/A:2 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:2-330 2479 atoms, 2537 bonds, 2 pseudobonds, 324 residues, 2 models selected > color (#!2 & sel) #1a8cf3ff > select #2/A:455-495 327 atoms, 336 bonds, 41 residues, 1 model selected > select #2/A:331-495 1249 atoms, 1273 bonds, 1 pseudobond, 157 residues, 2 models selected > color (#!2 & sel) #1a8cf3ff > select #2/A:330 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:2-330 2479 atoms, 2537 bonds, 2 pseudobonds, 324 residues, 2 models selected > color (#!2 & sel) #4eaff3ff > color (#!2 & sel) #6ac0f3ff > color (#!2 & sel) #97c3f3ff > color (#!2 & sel) #7cbdf3ff > color (#!2 & sel) #b4daf3ff > color (#!2 & sel) #b5dbf3ff > color (#!2 & sel) #8dbef3ff > ui tool show ""Show Sequence Viewer"" > sequence chain #2/C Destroying pre-existing alignment with identifier 2/C Alignment identifier is 2/C > select #2/B:159 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/B:3-159 1216 atoms, 1240 bonds, 1 pseudobond, 151 residues, 2 models selected > color (#!2 & sel) #ffc499ff > ui tool show ""Show Sequence Viewer"" > sequence chain #2/C Destroying pre-existing alignment with identifier 2/C Alignment identifier is 2/C > select #2/D:290-361 486 atoms, 496 bonds, 1 pseudobond, 64 residues, 2 models selected > select #2/D:2-361 2356 atoms, 2390 bonds, 3 pseudobonds, 318 residues, 2 models selected > color (#!2 & sel) #c3b8ffff > color (#!2 & sel) #aba1ecff > select #2/E:361 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/E:2-361 2694 atoms, 2737 bonds, 1 pseudobond, 354 residues, 2 models selected > color (#!2 & sel) #101116ff > color (#!2 & sel) #9da3d9ff > select #2/F:313-362 389 atoms, 397 bonds, 50 residues, 1 model selected > select #2/F:2-362 2755 atoms, 2800 bonds, 361 residues, 1 model selected > color sel #b1e899ff > color sel #729762ff > color sel #aade93ff > select #2/G:290-362 515 atoms, 525 bonds, 1 pseudobond, 66 residues, 2 models selected > select #2/G:2-362 2713 atoms, 2756 bonds, 1 pseudobond, 354 residues, 2 models selected > color (#!2 & sel) #8ce88aff > select #2/H:254-361 766 atoms, 783 bonds, 1 pseudobond, 100 residues, 2 models selected > select #2/H:2-361 2691 atoms, 2734 bonds, 1 pseudobond, 352 residues, 2 models selected > color (#!2 & sel) #91cf6eff > select #2/I:331-361 243 atoms, 247 bonds, 31 residues, 1 model selected > select #2/I:2-361 2671 atoms, 2715 bonds, 1 pseudobond, 351 residues, 2 models selected > color (#!2 & sel) #cbaba9ff > color (#!2 & sel) #ac9290ff > color (#!2 & sel) #e8c3c1ff > color (#!2 & sel) #ede9ecff > color (#!2 & sel) #eec8c7ff > color (#!2 & sel) #b99c9aff ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4.dev202203230115 (2022-03-23) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Locale: UTF-8 Qt version: PyQt6 6.2.3, Qt 6.2.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.3 (21E230) Kernel Version: Darwin 21.4.0 Time since boot: 1 day 1:56 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.5.30 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.36.3 ChimeraX-AtomicLibrary: 6.1.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.2 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4.dev202203230115 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.8 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.5 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.16.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 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: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.5.1 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.31.2 funcparserlib: 1.0.0a0 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.9.2 kiwisolver: 1.4.0 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.4 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.28 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.7 PyQt6-commercial: 6.2.3 PyQt6-sip: 13.2.0 PyQt6-WebEngine-commercial: 6.2.1 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 22.3.0 qtconsole: 5.2.2 QtPy: 2.0.1 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 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-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX