Opened 3 years ago

Closed 3 years ago

#8250 closed defect (limitation)

Crash in _adjust_surface_geometry

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x0000000200ace2c0 (most recent call first):
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 2219 in _adjust_surface_geometry
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 2195 in _calculate_contour_surface
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 2101 in update_surface
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 805 in _update_surfaces
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 782 in update_drawings
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume.py", line 4010 in _update_drawings
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 271 in check_for_drawing_change
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 65 in draw_new_frame
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
  File "/Applications/ChimeraX-1.4.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-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in 
  File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.4.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":"2023-01-02 17:08:24.00 -0500","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 13.1 (22C65)","roots_installed":0,"name":"ChimeraX","incident_id":"7C1C118B-F242-4DD6-BE4D-BE6CDD1ED5E9"}
{
  "uptime" : 12000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,4",
  "coalitionID" : 1935,
  "osVersion" : {
    "train" : "macOS 13.1",
    "build" : "22C65",
    "releaseType" : "User"
  },
  "captureTime" : "2023-01-02 17:07:06.4361 -0500",
  "incident" : "7C1C118B-F242-4DD6-BE4D-BE6CDD1ED5E9",
  "pid" : 2853,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-01-02 16:36:46.7731 -0500",
  "procStartAbsTime" : 253351864099,
  "procExitAbsTime" : 297021132705,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"9685953E-A792-5D68-8DB9-FE3533B0AA27","thirdParty":true},
  "parentProc" : "zsh",
  "parentPid" : 2577,
  "coalitionName" : "com.apple.Terminal",
  "crashReporterKey" : "426B9888-B885-3406-18D6-B38C6C33D789",
  "responsiblePid" : 2263,
  "responsibleProc" : "Terminal",
  "wakeTime" : 7232,
  "sleepWakeUUID" : "57E65D85-61E0-4B5B-8D8F-EA9FC971C261",
  "sip" : "enabled",
  "vmRegionInfo" : "0x7f7f16700010 is not in any region.  Bytes after previous region: 34548556496913  Bytes before following region: 8589934576\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_NANO              601318000000-601320000000 [128.0M] rw-\/rwx SM=PRV  \n--->  GAP OF 0x1f6df6700000 BYTES\n      MALLOC_LARGE             7f8116700000-7f811e700000 [128.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x00007f7f16700010","rawCodes":[1,140183814012944],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00007f7f16700010"},
  "ktriageinfo" : "VM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\nVM - pmap_enter retried due to resource shortage\n",
  "vmregioninfo" : "0x7f7f16700010 is not in any region.  Bytes after previous region: 34548556496913  Bytes before following region: 8589934576\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_NANO              601318000000-601320000000 [128.0M] rw-\/rwx SM=PRV  \n--->  GAP OF 0x1f6df6700000 BYTES\n      MALLOC_LARGE             7f8116700000-7f811e700000 [128.0M] rw-\/rwx SM=PRV  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"triggered":true,"id":131054,"threadState":{"flavor":"x86_THREAD_STATE","rbp":{"value":15141235539819185701},"r12":{"value":259},"rosetta":{"tmp2":{"value":140703430382112},"tmp1":{"value":140705833118076},"tmp0":{"value":18446744073709551615}},"rbx":{"value":8601264832,"symbolLocation":0,"symbol":"_main_thread"},"r8":{"value":11},"r15":{"value":22},"r10":{"value":8601264832,"symbolLocation":0,"symbol":"_main_thread"},"rdx":{"value":0},"rdi":{"value":15141235539819185701},"r9":{"value":15141235539819185701},"r13":{"value":0},"rflags":{"value":643},"rax":{"value":0},"rsp":{"value":5200433288},"r11":{"value":7},"rcx":{"value":0},"r14":{"value":11},"rsi":{"value":5200433288}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":33322,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":1},{"imageOffset":24443,"symbol":"pthread_kill","symbolLocation":263,"imageIndex":2},{"imageOffset":279856,"symbol":"raise","symbolLocation":26,"imageIndex":3},{"imageOffset":15389,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":4},{"imageOffset":0,"imageIndex":0},{"imageOffset":45936,"symbol":"mvm_allocate_pages","symbolLocation":313,"imageIndex":5},{"imageOffset":48721,"symbol":"large_malloc","symbolLocation":957,"imageIndex":5},{"imageOffset":8243,"symbol":"szone_malloc_should_clear","symbolLocation":245,"imageIndex":5},{"imageOffset":874585,"symbol":"PyArray_UpdateFlags","symbolLocation":233,"imageIndex":6},{"imageOffset":594226,"symbol":"PyArray_NewFromDescr_int","symbolLocation":1282,"imageIndex":6},{"imageOffset":596754,"symbol":"PyArray_New","symbolLocation":114,"imageIndex":6},{"imageOffset":140216129941840,"imageIndex":0}]},{"id":131056,"name":"com.apple.rosetta.exceptionserver","frames":[{"imageOffset":17940,"imageIndex":7},{"imageOffset":66864,"imageIndex":7},{"imageOffset":73520,"imageIndex":7}]},{"id":131059,"frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":8},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131060,"frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":8},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131061,"frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":8},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131062,"frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":8},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131063,"frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":8},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131064,"frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":8},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131065,"frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":8},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131066,"frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":8},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131067,"frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":3347615,"symbol":"blas_thread_server","symbolLocation":207,"imageIndex":8},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131117,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":44654,"symbol":"kevent64","symbolLocation":10,"imageIndex":1},{"imageOffset":66463178,"imageIndex":9},{"imageOffset":66462919,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":65964109,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131119,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66014559,"imageIndex":9},{"imageOffset":66017292,"imageIndex":9},{"imageOffset":66016125,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131120,"name":"Chrome_IOThread","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":44654,"symbol":"kevent64","symbolLocation":10,"imageIndex":1},{"imageOffset":66463178,"imageIndex":9},{"imageOffset":66462919,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":48397874,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131121,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66258831,"imageIndex":9},{"imageOffset":65429641,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131125,"name":"CompositorTileWorker1","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":66226363,"imageIndex":9},{"imageOffset":100635997,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131126,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66258831,"imageIndex":9},{"imageOffset":65429641,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131127,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":44654,"symbol":"kevent64","symbolLocation":10,"imageIndex":1},{"imageOffset":66463178,"imageIndex":9},{"imageOffset":66462919,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131128,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66258831,"imageIndex":9},{"imageOffset":65429641,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131129,"name":"VizCompositorThread","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66258831,"imageIndex":9},{"imageOffset":65429641,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131137,"name":"NetworkService","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":44654,"symbol":"kevent64","symbolLocation":10,"imageIndex":1},{"imageOffset":66463178,"imageIndex":9},{"imageOffset":66462919,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131138,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66258831,"imageIndex":9},{"imageOffset":65429641,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131139,"name":"ThreadPoolSingleThreadForegroundBlocking0","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66014559,"imageIndex":9},{"imageOffset":66017292,"imageIndex":9},{"imageOffset":66016365,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131171,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66258831,"imageIndex":9},{"imageOffset":65429641,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131182,"name":"com.apple.NSEventThread","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":520219,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":145,"imageIndex":10},{"imageOffset":514676,"symbol":"__CFRunLoopRun","symbolLocation":1387,"imageIndex":10},{"imageOffset":511631,"symbol":"CFRunLoopRunSpecific","symbolLocation":560,"imageIndex":10},{"imageOffset":1696409,"symbol":"_NSEventThread","symbolLocation":132,"imageIndex":11},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131201,"name":"MemoryInfra","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66258831,"imageIndex":9},{"imageOffset":65429641,"imageIndex":9},{"imageOffset":65925532,"imageIndex":9},{"imageOffset":65630200,"imageIndex":9},{"imageOffset":66065496,"imageIndex":9},{"imageOffset":66065898,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":131202,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking1","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66014559,"imageIndex":9},{"imageOffset":66016570,"imageIndex":9},{"imageOffset":66016173,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":133612,"name":"QFileInfoGatherer","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":16666,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":1},{"imageOffset":26593,"symbol":"_pthread_cond_wait","symbolLocation":1243,"imageIndex":2},{"imageOffset":2109867,"imageIndex":12},{"imageOffset":2109726,"symbol":"QWaitCondition::wait(QMutex*, QDeadlineTimer)","symbolLocation":94,"imageIndex":12},{"imageOffset":4541821,"symbol":"QFileInfoGatherer::run()","symbolLocation":125,"imageIndex":13},{"imageOffset":2067267,"imageIndex":12},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":133791,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":140705833118120,"imageIndex":0},{"imageOffset":5570,"symbol":"mach_msg2_trap","symbolLocation":10,"imageIndex":1},{"imageOffset":62980,"symbol":"mach_msg2_internal","symbolLocation":82,"imageIndex":1},{"imageOffset":34357,"symbol":"mach_msg_overwrite","symbolLocation":723,"imageIndex":1},{"imageOffset":6312,"symbol":"mach_msg","symbolLocation":19,"imageIndex":1},{"imageOffset":66259398,"imageIndex":9},{"imageOffset":66014559,"imageIndex":9},{"imageOffset":66017292,"imageIndex":9},{"imageOffset":66016269,"imageIndex":9},{"imageOffset":66229416,"imageIndex":9},{"imageOffset":25177,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":2},{"imageOffset":7291,"symbol":"thread_start","symbolLocation":15,"imageIndex":2}]},{"id":141414,"frames":[{"imageOffset":141436,"imageIndex":7}]}],
  "usedImages" : [
  {
    "size" : 0,
    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703430348800,
    "size" : 237560,
    "uuid" : "7c3dcc95-9f42-3c7c-8796-476ff67b9cf7",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703430586368,
    "size" : 49144,
    "uuid" : "5920e36f-53ec-33f0-b675-8ae48b58418c",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703429332992,
    "size" : 561152,
    "uuid" : "376f7cb7-6dd2-3e00-976f-77dd755bdb0d",
    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703430770688,
    "size" : 40952,
    "uuid" : "f314b62b-98f4-3a7c-8296-8739f8b6855a",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703428845568,
    "size" : 184320,
    "uuid" : "f609f029-bcd0-3a54-b48a-99b3ce8378ce",
    "path" : "\/usr\/lib\/system\/libsystem_malloc.dylib",
    "name" : "libsystem_malloc.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4461248512,
    "size" : 3964928,
    "uuid" : "94ced9bb-90b1-35c1-98bc-bbaa801637cc",
    "path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/core\/_multiarray_umath.cpython-39-darwin.so",
    "name" : "_multiarray_umath.cpython-39-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 140703126048768,
    "size" : 196608,
    "uuid" : "d592bc4a-4a21-348f-a406-e12f9cd2f27c",
    "path" : "\/usr\/libexec\/rosetta\/runtime",
    "name" : "runtime"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4539551744,
    "size" : 63488000,
    "uuid" : "10431d8f-5e3b-3bbc-abd5-81f6a73a5269",
    "path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5230186496,
    "size" : 165068800,
    "uuid" : "c9795830-14cd-3b40-983d-a3143cd9cbd9",
    "path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703430987776,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 4816896,
    "uuid" : "f3846a86-644b-3bcd-acce-fc7b751105c1",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1953.300"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703482130432,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 16809984,
    "uuid" : "00f4aa78-a19f-3a8e-9650-9f90b7beefd6",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2299.30.116"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4943290368,
    "size" : 5226496,
    "uuid" : "97d356c9-7652-3ff7-be10-198e30670243",
    "path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
    "name" : "QtCore"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5028675584,
    "size" : 6815744,
    "uuid" : "1d3e67c7-22f9-33ac-a03a-446da81fdc43",
    "path" : "\/Applications\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
    "name" : "QtGui"
  }
],
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=97.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=97.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               256K        2 \nActivity Tracing                   256K        1 \nCG backing stores                 3520K        4 \nCG image                          1324K       46 \nColorSync                          244K       28 \nCoreAnimation                     1720K       82 \nCoreGraphics                        12K        2 \nCoreImage                           24K        2 \nCoreServices                       624K        2 \nCoreUI image data                 5300K       39 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                            94.8G      926 \nMALLOC guard page                  192K       10 \nMALLOC_LARGE (reserved)          638.0M        1         reserved VM address space (unallocated)\nMALLOC_MEDIUM (reserved)           1.0G       10         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1332K      330 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               940K       94 \nRosetta Thread Context             940K       94 \nSTACK GUARD                          4K        1 \nStack                            142.0M       29 \nStack Guard                       56.1M       28 \nVM_ALLOCATE                      220.0M      317 \nVM_ALLOCATE (reserved)           224.1M       13         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            46.3M      745 \n__DATA_CONST                      40.3M      394 \n__DATA_DIRTY                      1845K      230 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       196.7M      144 \n__OBJC_RO                         65.4M        1 \n__OBJC_RW                         1985K        2 \n__TEXT                           891.2M      754 \ndyld private memory                416K        3 \nmapped file                        4.8G     1720 \nshared memory                     3016K       25 \nunshared pmap                     12.1M        7 \n===========                     =======  ======= \nTOTAL                            103.2G     6104 \nTOTAL, minus reserved VM space   101.4G     6104 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "6112d17137f5d11121dcd4e2",
      "factorPackIds" : {

      },
      "deploymentId" : 240000188
    },
    {
      "rolloutId" : "5fb4245a1bbfe8005e33a1e1",
      "factorPackIds" : {

      },
      "deploymentId" : 240000021
    }
  ],
  "experiments" : [

  ]
},
  "reportNotes" : [
  "dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open superOTV_DTT_chimerasession.py

ChimeraX cannot open a regular Chimera session. An exporter from Chimera  
to ChimeraX is being worked on but only handles molecules and molecular
surfaces  
(not volumes) at this time. If that is sufficient, use the latest Chimera  
daily build and its File->Export Scene menu item, and change the resulting  
dialog's "File Type" to ChimeraX.  

> open "/Users/cs/Documents/My writings/TVpaper/Maps/2023Jan2/OTV-Afit.pdb"
> "/Users/cs/Documents/My
> writings/TVpaper/Maps/2023Jan2/OTV_resampleDTTmap.mrc"
> "/Users/cs/Documents/My writings/TVpaper/Maps/2023Jan2/MTV-A.pdb"

Summary of feedback from opening /Users/cs/Documents/My
writings/TVpaper/Maps/2023Jan2/OTV-Afit.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 8 8 PRO B 75
LEU B 77 1 3  
Start residue of secondary structure not found: HELIX 9 9 LEU B 79 MET B 87 1
9  
Start residue of secondary structure not found: HELIX 10 10 ALA B 126 GLY B
131 1 6  
Start residue of secondary structure not found: HELIX 11 11 PRO B 220 SER B
222 1 3  
Start residue of secondary structure not found: HELIX 12 12 ASP B 390 GLN B
394 1 5  
28 messages similar to the above omitted  
  
Summary of feedback from opening /Users/cs/Documents/My
writings/TVpaper/Maps/2023Jan2/MTV-A.pdb  
---  
warnings | Ignored bad PDB record found on line 81  
  
  
Ignored bad PDB record found on line 82  
  
  
Ignored bad PDB record found on line 83  
ALLOWED : 6.25 %  
  
Ignored bad PDB record found on line 84  
CIS-PROLINE : 0.740740740741  
  
Ignored bad PDB record found on line 85  
CIS-GENERAL : 0.570206699929  
  
17 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 8 8 PRO B 75 LEU B 77 1
3  
Start residue of secondary structure not found: HELIX 9 9 LEU B 79 MET B 87 1
9  
Start residue of secondary structure not found: HELIX 10 10 PHE B 139 THR B
141 1 3  
Start residue of secondary structure not found: HELIX 11 11 PRO B 220 SER B
222 1 3  
Start residue of secondary structure not found: HELIX 12 12 ASP B 390 GLN B
394 1 5  
23 messages similar to the above omitted  
  
Chain information for OTV-Afit.pdb #1  
---  
Chain | Description  
A | No description available  
  
Opened OTV_resampleDTTmap.mrc as #2, grid size 146,146,146, pixel 1.1, shown
at level 4.17, step 1, values float32  
Chain information for MTV-A.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open "/Users/cs/Documents/My writings/TVpaper/Maps/comparewithDTT/cutABC-
> DTTmatchtonative.mrc"

Opened cutABC-DTTmatchtonative.mrc as #4, grid size 146,146,146, pixel 1.1,
shown at level 18.1, step 1, values float32  

> volume #2 level 3.727

> volume #4 level 10.65

> set bgColor white

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

Populating font family aliases took 187 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

> save "/Users/cs/Documents/My
> writings/TVpaper/Maps/2023Jan2/chimeraxsession.cxs" includeMaps true

> hide #!4 models

> hide #3 models

> surface zone #2 nearAtoms #1/A:284

> hide #1

> hide #1 models

> show #1/A:284

> heteroatom

Unknown command: heteroatom  

> heteroatomvolume #2 subdivide true subdivisionlevels 2

Unknown command: heteroatomvolume #2 subdivide true subdivisionlevels 2  

> volume #2 subdivideSurface true subdivisionLevels 2

> show #1 models

> volume #2 subdivideSurface true

> volume #!2 style mesh

> volume #2 color #8b83bf

> volume #2 color #a67fbf

> volume #2 color #bf5cb1

> volume #2 color #bf4e92

> volume #2 color #12070e

> volume #2 subdivideSurface true subdivisionLevels 2

> surface zone #2 nearAtoms #1/A:280-287

> volume #2 color #8f306d

> volume #2 color #4a878f

> volume #2 color #68808f

> show #3 models

> hide #3 models

> label #1/A:284

> heteroatom

Unknown command: heteroatom  

> select #1/A:284

8 atoms, 7 bonds, 1 residue, 1 model selected  

> view sel

> ~select

Nothing selected  

> select #1/A:284

8 atoms, 7 bonds, 1 residue, 1 model selected  

> view sel

> clip far 10

> clip far 20

> view sel

> ui tool show "Side View"

> ~select

Nothing selected  

> volume #2 color #54849f

> volume #2 color #729f96

> volume #2 color #9f2a3a

> volume #2 color #9f8b83

> show #1/A:283-286

> show #1/A:282-286

> select #1/A:282-286

34 atoms, 34 bonds, 5 residues, 1 model selected  

> style sel stick

Changed 34 atom styles  

> color #1/A:282-286 byatom

> color sel byhetero

> volume #2 subdivideSurface true subdivisionLevels 6


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,4
      Model Number: Z15K0010CLL/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 8419.60.44
      OS Loader Version: 8419.60.44

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 2 days, 2 hours, 35 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      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: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    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: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    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: 1.2
    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: 1.1.1
    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: 1.9
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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-StarMap: 1.1.70
    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: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    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: 4.10.0
    kiwisolver: 1.4.2
    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: 1.5.5
    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: 3.0.29
    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: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    pyqtgraph: 0.13.1
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    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

Change History (2)

comment:1 by pett, 3 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in _adjust_surface_geometry

comment:2 by Tom Goddard, 3 years ago

Resolution: → limitation
Status: assigned → closed

Memory allocation failed when trying to subdivide volume surface making it have 46 = 4096 times more triangles.

volume #2 subdivideSurface true subdivisionLevels 6

Might protect against this if it is reported more times.

Note: See TracTickets for help on using tickets.