Changes between Initial Version and Version 1 of Ticket #7286


Ignore:
Timestamp:
Jul 15, 2022, 10:19:46 AM (3 years ago)
Author:
Eric Pettersen
Comment:

No Python backtrace. Was using 11.7GB at the time.

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #7286

    • Property Cc Tom Goddard added
    • Property Component Unassigned → Core
    • Property Owner set to Eric Pettersen
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → accepted
    • Property Summary ChimeraX bug report submission → Unknown crash

  • Ticket #7286 – Description

    initial v1  
    66Last time you used ChimeraX it crashed.
    77Please describe steps that led to the crash here.
     8
     9
     10{"app_name":"ChimeraX","timestamp":"2022-07-14 13:47:52.00 +0200","app_version":"","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"","platform":1,"share_with_app_devs":0,"is_first_party":1,"bug_type":"309","os_version":"macOS 12.4 (21F79)","incident_id":"B162DD4D-E8C7-47BD-95F1-AD5E9DBA6DB5","name":"ChimeraX"}
     11{
     12  "uptime" : 1400000,
     13  "procLaunch" : "2022-07-07 16:16:48.3421 +0200",
     14  "procRole" : "Background",
     15  "version" : 2,
     16  "userID" : 501,
     17  "deployVersion" : 210,
     18  "modelCode" : "MacBookPro17,1",
     19  "procStartAbsTime" : 32037086705931,
     20  "coalitionID" : 73622,
     21  "osVersion" : {
     22    "train" : "macOS 12.4",
     23    "build" : "21F79",
     24    "releaseType" : "User"
     25  },
     26  "captureTime" : "2022-07-14 13:47:51.4949 +0200",
     27  "incident" : "B162DD4D-E8C7-47BD-95F1-AD5E9DBA6DB5",
     28  "bug_type" : "309",
     29  "pid" : 92276,
     30  "procExitAbsTime" : 33778630527872,
     31  "translated" : true,
     32  "cpuType" : "X86-64",
     33  "procName" : "ChimeraX",
     34  "procPath" : "\/private\/var\/folders\/*\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
     35  "parentProc" : "launchd",
     36  "parentPid" : 1,
     37  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
     38  "crashReporterKey" : "BB9D28C0-3EF2-B744-F9A6-E850B445ECA8",
     39  "wakeTime" : 2302,
     40  "sleepWakeUUID" : "B630B6E8-4B69-4705-B59E-EB3777D6ECE4",
     41  "sip" : "enabled",
     42  "vmRegionInfo" : "0x10adcc1d0 is in 0x10abcd000-0x10ae36000;  bytes after start: 2093520  bytes before end: 433711\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      Rosetta Generic             10abcc000-10abcd000    [    4K] rw-\/rwx SM=PRV  \n--->  mapped file                 10abcd000-10ae36000    [ 2468K] r-x\/rwx SM=COW  ...t_id=a7219d71\n      mapped file                 10ae36000-10ae70000    [  232K] rw-\/rwx SM=COW  ...t_id=a3a1b271",
     43  "isCorpse" : 1,
     44  "exception" : {"codes":"0x000000000000000a, 0x000000010adcc1d0","rawCodes":[10,4477206992],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x000000010adcc1d0"},
     45  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"exc handler","byPid":92276},
     46  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
     47  "vmregioninfo" : "0x10adcc1d0 is in 0x10abcd000-0x10ae36000;  bytes after start: 2093520  bytes before end: 433711\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      Rosetta Generic             10abcc000-10abcd000    [    4K] rw-\/rwx SM=PRV  \n--->  mapped file                 10abcd000-10ae36000    [ 2468K] r-x\/rwx SM=COW  ...t_id=a7219d71\n      mapped file                 10ae36000-10ae70000    [  232K] rw-\/rwx SM=COW  ...t_id=a3a1b271",
     48  "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},
     49  "faultingThread" : 0,
     50  "threads" : [{"triggered":true,"id":8073779,"threadState":{"flavor":"x86_THREAD_STATE","rbp":{"value":140647965425568},"r12":{"value":0},"rosetta":{"tmp2":{"value":140703288624800},"tmp1":{"value":4482039264},"tmp0":{"value":140705714310612}},"rbx":{"value":4477872336},"r8":{"value":4474843272},"r15":{"value":4477207001},"r10":{"value":8628471468,"symbolLocation":172,"symbol":"_main_thread"},"rdx":{"value":4477207001},"rdi":{"value":4477206992},"r9":{"value":14176809715294958669},"r13":{"value":10},"rflags":{"value":514},"rax":{"value":18446744073709551615},"rsp":{"value":140647965425568},"r11":{"value":105553176290856},"rcx":{"value":4477207001},"r14":{"value":13},"rsi":{"value":4477163155}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":5810,"symbol":"_platform_strlen","symbolLocation":18,"imageIndex":0},{"imageOffset":4477030343,"imageIndex":1},{"imageOffset":15869,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":0},{"imageOffset":0,"imageIndex":1},{"imageOffset":515415,"symbol":"__CFRunLoopRun","symbolLocation":1667,"imageIndex":2},{"imageOffset":512020,"symbol":"CFRunLoopRunSpecific","symbolLocation":562,"imageIndex":2},{"imageOffset":140703441475046,"imageIndex":1},{"imageOffset":140703441474378,"imageIndex":1},{"imageOffset":140703441473765,"imageIndex":1},{"imageOffset":140703332823549,"imageIndex":1},{"imageOffset":140703332817082,"imageIndex":1},{"imageOffset":140703332761449,"imageIndex":1},{"imageOffset":5042853004,"imageIndex":1},{"imageOffset":4905231638,"imageIndex":1},{"imageOffset":4905194469,"imageIndex":1},{"imageOffset":4963305738,"imageIndex":1},{"imageOffset":4475631389,"imageIndex":1},{"imageOffset":4475372983,"imageIndex":1},{"imageOffset":4476259996,"imageIndex":1},{"imageOffset":4476248738,"imageIndex":1},{"imageOffset":4475374888,"imageIndex":1},{"imageOffset":4475383146,"imageIndex":1},{"imageOffset":4476259852,"imageIndex":1},{"imageOffset":4476248738,"imageIndex":1},{"imageOffset":4476263171,"imageIndex":1},{"imageOffset":4475374769,"imageIndex":1},{"imageOffset":4476259852,"imageIndex":1},{"imageOffset":4476248907,"imageIndex":1},{"imageOffset":4476263171,"imageIndex":1},{"imageOffset":4476222891,"imageIndex":1},{"imageOffset":4476210194,"imageIndex":1},{"imageOffset":4475629603,"imageIndex":1},{"imageOffset":4476259852,"imageIndex":1},{"imageOffset":4476248907,"imageIndex":1},{"imageOffset":4476263171,"imageIndex":1},{"imageOffset":4475374769,"imageIndex":1},{"imageOffset":4476259852,"imageIndex":1},{"imageOffset":4476248907,"imageIndex":1},{"imageOffset":4476263171,"imageIndex":1},{"imageOffset":4475374769,"imageIndex":1},{"imageOffset":4476680304,"imageIndex":1},{"imageOffset":4476678023,"imageIndex":1},{"imageOffset":4476679567,"imageIndex":1},{"imageOffset":4476679323,"imageIndex":1},{"imageOffset":4330585544,"imageIndex":1},{"imageOffset":21790,"symbol":"start","symbolLocation":462,"imageIndex":3}]},{"id":8074026,"name":"com.apple.rosetta.exceptionserver","frames":[{"imageOffset":18884,"imageIndex":4},{"imageOffset":74848,"imageIndex":4},{"imageOffset":81624,"imageIndex":4}]},{"id":8076259,"name":"ThreadPoolServiceThread","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":43210,"symbol":"kevent64","symbolLocation":10,"imageIndex":5},{"imageOffset":5258102218,"imageIndex":1},{"imageOffset":5258101959,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5257603149,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076262,"name":"Chrome_IOThread","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":43210,"symbol":"kevent64","symbolLocation":10,"imageIndex":5},{"imageOffset":5258102218,"imageIndex":1},{"imageOffset":5258101959,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5240036914,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076263,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257897871,"imageIndex":1},{"imageOffset":5257068681,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076267,"name":"CompositorTileWorker1","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":5},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":6},{"imageOffset":5257865403,"imageIndex":1},{"imageOffset":5292275037,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076268,"name":"Chrome_InProcGpuThread","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257897871,"imageIndex":1},{"imageOffset":5257068681,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076269,"name":"Chrome_ChildIOThread","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":43210,"symbol":"kevent64","symbolLocation":10,"imageIndex":5},{"imageOffset":5258102218,"imageIndex":1},{"imageOffset":5258101959,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076270,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257897871,"imageIndex":1},{"imageOffset":5257068681,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076271,"name":"VizCompositorThread","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257897871,"imageIndex":1},{"imageOffset":5257068681,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076279,"name":"NetworkService","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":43210,"symbol":"kevent64","symbolLocation":10,"imageIndex":5},{"imageOffset":5258102218,"imageIndex":1},{"imageOffset":5258101959,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076280,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257897871,"imageIndex":1},{"imageOffset":5257068681,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076281,"name":"ThreadPoolSingleThreadForegroundBlocking0","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257653599,"imageIndex":1},{"imageOffset":5257656332,"imageIndex":1},{"imageOffset":5257655405,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076399,"name":"NetworkConfigWatcher","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257897871,"imageIndex":1},{"imageOffset":5257068681,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076459,"name":"com.apple.NSEventThread","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":521536,"symbol":"__CFRunLoopServiceMachPort","symbolLocation":319,"imageIndex":2},{"imageOffset":515024,"symbol":"__CFRunLoopRun","symbolLocation":1276,"imageIndex":2},{"imageOffset":512020,"symbol":"CFRunLoopRunSpecific","symbolLocation":562,"imageIndex":2},{"imageOffset":140703334321182,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076463,"name":"MemoryInfra","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257897871,"imageIndex":1},{"imageOffset":5257068681,"imageIndex":1},{"imageOffset":5257564572,"imageIndex":1},{"imageOffset":5257269240,"imageIndex":1},{"imageOffset":5257704536,"imageIndex":1},{"imageOffset":5257704938,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8076464,"name":"ThreadPoolSingleThreadSharedBackgroundBlocking1","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257653599,"imageIndex":1},{"imageOffset":5257655610,"imageIndex":1},{"imageOffset":5257655213,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8369405,"frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":5},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":6},{"imageOffset":4571468959,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8369406,"frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":5},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":6},{"imageOffset":4571468959,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8369407,"frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":5},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":6},{"imageOffset":4571468959,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8369408,"frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":5},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":6},{"imageOffset":4571468959,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8369409,"frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":5},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":6},{"imageOffset":4571468959,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8369410,"frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":5},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":6},{"imageOffset":4571468959,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8369411,"frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":5},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":6},{"imageOffset":4571468959,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8839177,"name":"QFileInfoGatherer","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":5},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":6},{"imageOffset":4906860971,"imageIndex":1},{"imageOffset":4906860830,"imageIndex":1},{"imageOffset":4994669949,"imageIndex":1},{"imageOffset":4906818371,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":8876399,"name":"QFileInfoGatherer","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":17386,"symbol":"__psynch_cvwait","symbolLocation":10,"imageIndex":5},{"imageOffset":27247,"symbol":"_pthread_cond_wait","symbolLocation":1249,"imageIndex":6},{"imageOffset":4906860971,"imageIndex":1},{"imageOffset":4906860830,"imageIndex":1},{"imageOffset":4994669949,"imageIndex":1},{"imageOffset":4906818371,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":9234314,"name":"ThreadPoolForegroundWorker","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257653599,"imageIndex":1},{"imageOffset":5257656332,"imageIndex":1},{"imageOffset":5257655309,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":9308548,"name":"ThreadPoolBackgroundWorker","frames":[{"imageOffset":140705710205248,"imageIndex":1},{"imageOffset":6522,"symbol":"mach_msg_trap","symbolLocation":10,"imageIndex":5},{"imageOffset":7400,"symbol":"mach_msg","symbolLocation":56,"imageIndex":5},{"imageOffset":5257898438,"imageIndex":1},{"imageOffset":5257653599,"imageIndex":1},{"imageOffset":5257656332,"imageIndex":1},{"imageOffset":5257655165,"imageIndex":1},{"imageOffset":5257868456,"imageIndex":1},{"imageOffset":25825,"symbol":"_pthread_start","symbolLocation":125,"imageIndex":6},{"imageOffset":8043,"symbol":"thread_start","symbolLocation":15,"imageIndex":6}]},{"id":9339739,"frames":[{"imageOffset":141332,"imageIndex":4}]},{"id":9339862,"frames":[{"imageOffset":141332,"imageIndex":4}]},{"id":9339863,"frames":[{"imageOffset":141332,"imageIndex":4}]},{"id":9339864,"frames":[{"imageOffset":141332,"imageIndex":4}]},{"id":9339865,"frames":[{"imageOffset":141332,"imageIndex":4}]},{"id":9339866,"frames":[{"imageOffset":141332,"imageIndex":4}]},{"id":9339867,"frames":[{"imageOffset":141332,"imageIndex":4}]},{"id":9339870,"frames":[{"imageOffset":141332,"imageIndex":4}]},{"id":9339871,"frames":[{"imageOffset":141332,"imageIndex":4}]}],
     51  "usedImages" : [
     52  {
     53    "source" : "P",
     54    "arch" : "x86_64",
     55    "base" : 140703288619008,
     56    "size" : 40960,
     57    "uuid" : "f6cad74b-ec4d-3ff9-80f3-b066753f9fab",
     58    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
     59    "name" : "libsystem_platform.dylib"
     60  },
     61  {
     62    "size" : 0,
     63    "source" : "A",
     64    "base" : 0,
     65    "uuid" : "00000000-0000-0000-0000-000000000000"
     66  },
     67  {
     68    "source" : "P",
     69    "arch" : "x86_64",
     70    "base" : 140703288836096,
     71    "CFBundleShortVersionString" : "6.9",
     72    "CFBundleIdentifier" : "com.apple.CoreFoundation",
     73    "size" : 5246976,
     74    "uuid" : "9c8908f2-e5e0-35b7-9f41-fdf8d7476d8b",
     75    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
     76    "name" : "CoreFoundation",
     77    "CFBundleVersion" : "1863"
     78  },
     79  {
     80    "source" : "P",
     81    "arch" : "x86_64",
     82    "base" : 8627945472,
     83    "size" : 442368,
     84    "uuid" : "b70ce1ec-b902-3852-8268-05de00bfa8d5",
     85    "path" : "\/usr\/lib\/dyld",
     86    "name" : "dyld"
     87  },
     88  {
     89    "source" : "P",
     90    "arch" : "arm64",
     91    "base" : 140703126843392,
     92    "size" : 196608,
     93    "uuid" : "0ee8ce32-639c-316a-9551-dab9a2e0c8a5",
     94    "path" : "\/usr\/libexec\/rosetta\/runtime",
     95    "name" : "runtime"
     96  },
     97  {
     98    "source" : "P",
     99    "arch" : "x86_64",
     100    "base" : 140703288291328,
     101    "size" : 229376,
     102    "uuid" : "61711d11-e776-3bc3-b9a2-6f9f37cb8499",
     103    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
     104    "name" : "libsystem_kernel.dylib"
     105  },
     106  {
     107    "source" : "P",
     108    "arch" : "x86_64",
     109    "base" : 140703288520704,
     110    "size" : 49152,
     111    "uuid" : "bc574849-1aae-31e7-b350-916dda999d97",
     112    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
     113    "name" : "libsystem_pthread.dylib"
     114  }
     115],
     116  "sharedCache" : {
     117  "base" : 140703285264384,
     118  "size" : 15220686848,
     119  "uuid" : "53b6853f-0bc3-33f5-be72-1aca3a188ff8"
     120},
     121  "vmSummary" : "ReadOnly portion of Libraries: Total=205.8M resident=0K(0%) swapped_out_or_unallocated=205.8M(100%)\nWritable regions: Total=4.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.4G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 9552K       11 \nCG image                           928K       83 \nColorSync                          236K       28 \nCoreAnimation                     3280K       84 \nCoreGraphics                        52K       12 \nCoreServices                       624K        2 \nCoreUI image data                 5376K       46 \nFoundation                          36K        2 \nKernel Alloc Once                 1296K        3 \nMALLOC                             3.1G      905 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)         768.0M        8         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1688K      419 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               720K       72 \nRosetta Thread Context             720K       72 \nSTACK GUARD                         36K        9 \nStack                            145.6M       36 \nStack Guard                       56.1M       27 \nVM_ALLOCATE                      172.4M      252 \nVM_ALLOCATE (reserved)            96.1M       11         reserved VM address space (unallocated)\n__DATA                             355K       46 \n__DATA_CONST                      3033K       40 \n__DATA_DIRTY                        79K       24 \n__LINKEDIT                       192.9M        7 \n__OBJC_RO                         82.7M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                            13.0M       50 \n__UNICODE                          592K        1 \ndyld private memory               1184K        3 \nmapped file                        7.0G     1038 \nshared memory                     5620K       42 \nunshared pmap                     12.6M        9 \n===========                     =======  ======= \nTOTAL                             11.7G     3370 \nTOTAL, minus reserved VM space    10.9G     3370 \n",
     122  "legacyInfo" : {
     123  "threadTriggered" : {
     124    "name" : "CrBrowserMain",
     125    "queue" : "com.apple.main-thread"
     126  }
     127},
     128  "trialInfo" : {
     129  "rollouts" : [
     130    {
     131      "rolloutId" : "60186475825c62000ccf5450",
     132      "factorPackIds" : {
     133        "SIRI_VALUE_INFERENCE_CONTACT_RESOLUTION" : "62bdc4218fe09c1632d841e9"
     134      },
     135      "deploymentId" : 240000023
     136    },
     137    {
     138      "rolloutId" : "5fc94383418129005b4e9ae0",
     139      "factorPackIds" : {
     140
     141      },
     142      "deploymentId" : 240000401
     143    }
     144  ],
     145  "experiments" : [
     146
     147  ]
     148}
     149}
     150===== Log before crash start =====
     151Startup Messages 
     152--- 
     153note | available bundle cache has not been initialized yet 
     154 
     155UCSF ChimeraX version: 1.4 (2022-06-03) 
     156© 2016-2022 Regents of the University of California. All rights reserved. 
     157How to cite UCSF ChimeraX 
     158
     159> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4_optimized.mol2"
     160
     161Opened A4H4_optimized.mol2 containing 1 structures (336 atoms, 360 bonds) 
     162
     163> set bgColor white
     164
     165> style balls
     166
     167Expected a keyword 
     168
     169> style ball
     170
     171Changed 336 atom styles 
     172
     173> hide H
     174
     175Drag select of 15 atoms, 15 bonds 
     176Drag select of 15 atoms, 16 bonds 
     177
     178> name frozen Amines sel
     179
     180> color C orange
     181
     182> color Amines orchid
     183
     184> select clear
     185
     186> lighting soft
     187
     188> lighting shadows true intensity 0.5
     189
     190> graphics silhouettes true
     191
     192> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4 full on
     193> picture.png" transparentBackground true
     194
     195> style sphere
     196
     197Changed 336 atom styles 
     198
     199> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4 sphere window
     200> view.png" transparentBackground true
     201
     202> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4.cxs"
     203
     204> close session
     205
     206> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3 optimized.mol2"
     207
     208Opened A4H1F3 optimized.mol2 containing 1 structures (336 atoms, 360 bonds) 
     209
     210> hide H
     211
     212> style balls
     213
     214Expected a keyword 
     215
     216> style ball
     217
     218Changed 336 atom styles 
     219Drag select of 15 atoms, 16 bonds 
     220Drag select of 15 atoms, 17 bonds 
     221Drag select of 15 atoms, 16 bonds 
     222
     223> name frozen Amines sel
     224
     225> select clear
     226
     227> select /?:1@@serial_number=-1
     228
     229336 atoms, 360 bonds, 1 residue, 1 model selected 
     230
     231> select clear
     232
     233Drag select of 1 atoms 
     234
     235> select add /?:1@@serial_number=-1
     236
     237336 atoms, 360 bonds, 1 residue, 1 model selected 
     238
     239> select clear
     240
     241Drag select of 1 atoms 
     242Drag select of 1 atoms, 2 bonds 
     243Drag select of 2 atoms, 1 bonds 
     244Drag select of 1 atoms, 1 bonds 
     245Drag select of 2 atoms, 2 bonds 
     246Drag select of 2 atoms, 1 bonds 
     247Drag select of 1 atoms 
     248Drag select of 2 atoms, 3 bonds 
     249Drag select of 2 atoms, 1 bonds 
     250Drag select of 2 atoms, 2 bonds 
     251Drag select of 1 atoms, 1 bonds 
     252
     253> name frozen H-aldehyde sel
     254
     255> color C dodger blue
     256
     257> color Amines orchid
     258
     259> color H-aldehyde orange
     260
     261> color F pale green
     262
     263> select clear
     264
     265> lighting soft
     266
     267> lighting shadows true intensity 0.5
     268
     269> graphics silhouettes false
     270
     271> graphics silhouettes true
     272
     273> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3 full on.png"
     274> transparentBackground true
     275
     276> style sphere
     277
     278Changed 336 atom styles 
     279
     280> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3 sphere window
     281> view.png" transparentBackground true
     282
     283> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3.cxs"
     284
     285> close session
     286
     287> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2 optimized.mol2"
     288
     289Opened A4H2F2 optimized.mol2 containing 1 structures (336 atoms, 360 bonds) 
     290
     291> hide H
     292
     293> style ball
     294
     295Changed 336 atom styles 
     296Drag select of 15 atoms, 15 bonds 
     297Drag select of 15 atoms, 16 bonds 
     298
     299> name frozen Amines sel
     300
     301> select clear
     302
     303Drag select of 27 atoms, 31 bonds 
     304Drag select of 1 atoms 
     305Drag select of 25 atoms, 30 bonds 
     306Drag select of 1 atoms, 1 bonds 
     307
     308> name frozen H-Aldehyde sel
     309
     310> color C dodger blue
     311
     312> color Amines orchid
     313
     314> color H-Aldehyde orange
     315
     316> select clear
     317
     318> lighting soft
     319
     320> lighting shadows true intensity 0.5
     321
     322> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2 full on.png"
     323> transparentBackground true
     324
     325> show H
     326
     327> style sphere
     328
     329Changed 336 atom styles 
     330
     331> hide H
     332
     333> show H
     334
     335> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2 window view.png"
     336> transparentBackground true
     337
     338> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2.cxs"
     339
     340> close session
     341
     342> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1 optimized.mol2"
     343
     344Opened A4H3F1 optimized.mol2 containing 1 structures (336 atoms, 360 bonds) 
     345
     346> hide H
     347
     348> style ball
     349
     350Changed 336 atom styles 
     351Drag select of 15 atoms, 17 bonds 
     352Drag select of 15 atoms, 16 bonds 
     353Drag select of 15 atoms, 15 bonds 
     354
     355> name frozen Amines sel
     356
     357> select clear
     358
     359Drag select of 11 atoms, 12 bonds 
     360Drag select of 19 atoms, 21 bonds 
     361Drag select of 1 atoms 
     362Drag select of 2 atoms, 1 bonds 
     363Drag select of 11 atoms, 13 bonds 
     364Drag select of 1 atoms, 1 bonds 
     365Drag select of 1 atoms 
     366
     367> color frozen F-Aldehyde sel
     368
     369Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
     370'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
     371or a keyword 
     372
     373> name frozen F-Aldehyde sel
     374
     375> color C orange
     376
     377> color F-Aldehyde dodger blue
     378
     379> color F pale green
     380
     381> color Amines orchid
     382
     383> select clear
     384
     385> lighting soft
     386
     387> lighting shadows true intensity 0.5
     388
     389> graphics silhouettes false
     390
     391> graphics silhouettes true
     392
     393> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1 full on.png"
     394> transparentBackground true
     395
     396> style sphere
     397
     398Changed 336 atom styles 
     399
     400> show H
     401
     402> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1 window view.png"
     403> transparentBackground true
     404
     405> save "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1.cxs"
     406
     407> close session
     408
     409> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4.cxs" format
     410> session
     411
     412opened ChimeraX session 
     413
     414> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H4 cavity_cav1.dx"
     415
     416Opened A4H4 cavity_cav1.dx as #2, grid size 96,97,98, pixel 0.2, shown at
     417level -6,6, step 1, values float32 
     418
     419> volume #2 level 0.3878 level 6
     420
     421> volume #2 color #ff9f3f color #b2b2b2
     422
     423> volume #2 color #ff9856 color #b2b2b2
     424
     425> volume #2 color #ff9f3f color #b2b2b2
     426
     427> style stick
     428
     429Changed 336 atom styles 
     430
     431> volume #2 level 3.803 level 6
     432
     433> movie record
     434
     435> turn y 2 180
     436
     437> wait 180
     438
     439> movie encode /Users/tomkunde/Desktop/movie3.mp4
     440
     441Movie saved to /Users/tomkunde/Desktop/movie3.mp4 
     442 
     443
     444> close session
     445
     446> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3.cxs" format
     447> session
     448
     449opened ChimeraX session 
     450
     451> style stick
     452
     453Changed 336 atom styles 
     454
     455> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3 cavity_cav1.dx"
     456
     457Opened A4H1F3 cavity_cav1.dx as #2, grid size 94,92,85, pixel 0.2, shown at
     458level -6,6, step 1, values float32 
     459
     460> volume #2 level 0.2585 level 6
     461
     462> volume #2 color #8ed243 color #ffffb2
     463
     464> volume #2 color #ff9f3f color #ffffb2
     465
     466> volume #2 color #ffd159 color #ffffb2
     467
     468> volume #2 level 0.377 level 6
     469
     470> movie record
     471
     472> turn y 2 180
     473
     474> wait 180
     475
     476> movie encode /Users/tomkunde/Desktop/movie4.mp4
     477
     478Movie saved to /Users/tomkunde/Desktop/movie4.mp4 
     479 
     480
     481> close session
     482
     483> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2.cxs" format
     484> session
     485
     486opened ChimeraX session 
     487
     488> style stick
     489
     490Changed 336 atom styles 
     491
     492> hide H
     493
     494> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H2F2 cavity_cav1.dx"
     495
     496Opened A4H2F2 cavity_cav1.dx as #2, grid size 98,91,93, pixel 0.2, shown at
     497level -6,6, step 1, values float32 
     498
     499> volume #2 level 0.5494 level 6
     500
     501> volume #2 color #e9ff52 color #b2ffff
     502
     503> volume #2 color #cbdf47 color #b2ffff
     504
     505> movie record
     506
     507> turn y 2 180
     508
     509> wait 180
     510
     511> movie encode /Users/tomkunde/Desktop/movie5.mp4
     512
     513Movie saved to /Users/tomkunde/Desktop/movie5.mp4 
     514 
     515
     516> close session
     517
     518> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1.cxs" format
     519> session
     520
     521opened ChimeraX session 
     522
     523> style stick
     524
     525Changed 336 atom styles 
     526
     527> hide H
     528
     529> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H3F1 cavity_cav1.dx"
     530
     531Opened A4H3F1 cavity_cav1.dx as #2, grid size 81,100,97, pixel 0.2, shown at
     532level -6,6, step 1, values float32 
     533
     534> volume #2 level 1.228 level 6
     535
     536> volume #2 color #ff9f3f color #b2b2ff
     537
     538> volume #2 color #a6ff53 color #b2b2ff
     539
     540> volume #2 color #8ad445 color #b2b2ff
     541
     542> movie record
     543
     544> turn y 2 180
     545
     546> wait 180
     547
     548> movie encode /Users/tomkunde/Desktop/movie6.mp4
     549
     550Movie saved to /Users/tomkunde/Desktop/movie6.mp4 
     551 
     552
     553> close session
     554
     555> open "/Users/tomkunde/Documents/Work/MOL-files Cages/Stacked FF24 .cxs"
     556
     557opened ChimeraX session 
     558
     559> open "/Users/tomkunde/Documents/Work/Crystal structures/FF24 cavity
     560> maps_cav1.dx"
     561
     562Opened FF24 cavity maps_cav1.dx as #2, grid size 29,29,36, pixel 0.2, shown at
     563level -4,4, step 1, values float32 
     564
     565> volume #2 level 0.3555 level 4
     566
     567> volume #2 color #dffb81 color #ffb2ff
     568
     569> open "/Users/tomkunde/Documents/Work/Crystal structures/FF24 cavity
     570> maps_cav2.dx"
     571
     572Opened FF24 cavity maps_cav2.dx as #3, grid size 27,24,29, pixel 0.2, shown at
     573level -4,4, step 1, values float32 
     574
     575> volume #3 level 1.928 level 4
     576
     577> volume #3 color #dffb81 color #ffb2b2
     578
     579> open "/Users/tomkunde/Documents/Work/Crystal structures/FF24 cavity
     580> maps_cav3.dx" "/Users/tomkunde/Documents/Work/Crystal structures/FF24 cavity
     581> maps_cav5.dx" "/Users/tomkunde/Documents/Work/Crystal structures/FF24 cavity
     582> maps_cav4.dx"
     583
     584Opened FF24 cavity maps_cav3.dx as #4.1, grid size 25,26,21, pixel 0.2, shown
     585at level -4,4, step 1, values float32 
     586Opened FF24 cavity maps_cav5.dx as #4.2, grid size 9,19,16, pixel 0.2, shown
     587at level -4,4, step 1, values float32 
     588Opened FF24 cavity maps_cav4.dx as #4.3, grid size 16,22,20, pixel 0.2, shown
     589at level -4,4, step 1, values float32 
     590
     591> volume #4.1 level 0.4436 level 4
     592
     593> volume #4.1 color #dffb81 color #b2ffb2
     594
     595> volume #4.2 level 0.61 level 4
     596
     597> volume #4.2 color #dffb81 color #e5bf99
     598
     599> volume #4.3 level 0.4104 level 4
     600
     601> volume #4.3 color #dffb81 color #99bfe5
     602
     603> style stick
     604
     605Changed 396 atom styles 
     606
     607> movie record
     608
     609> turn y 2 180
     610
     611> wait 180
     612
     613> movie encode /Users/tomkunde/Desktop/movie7.mp4
     614
     615Movie saved to /Users/tomkunde/Desktop/movie7.mp4 
     616 
     617
     618> open "/Users/tomkunde/Documents/Work/Crystal structures/FF24 H2
     619> cavity_cav1.dx"
     620
     621Opened FF24 H2 cavity_cav1.dx as #5, grid size 85,55,56, pixel 0.2, shown at
     622level -6,6, step 1, values float32 
     623
     624> hide #!4 models
     625
     626> hide #!3 models
     627
     628> hide #!2 models
     629
     630> volume #5 level 0.6654 level 6
     631
     632> volume #5 color #ff6875 color #cccc99
     633
     634> movie record
     635
     636> turn y 2 180
     637
     638> wait 180
     639
     640> movie encode /Users/tomkunde/Desktop/movie8.mp4
     641
     642Movie saved to /Users/tomkunde/Desktop/movie8.mp4 
     643 
     644
     645> close session
     646
     647> open "/Users/tomkunde/Documents/Work/Untitled Folder/GC2_optimized.mol"
     648
     649> hdie H
     650
     651Unknown command: hdie H 
     652
     653> hide H
     654
     655> style ball
     656
     657Changed 336 atom styles 
     658Drag select of 15 atoms, 16 bonds 
     659Drag select of 15 atoms, 17 bonds 
     660Drag select of 15 atoms, 18 bonds 
     661Drag select of 15 atoms, 15 bonds 
     662
     663> name frozen Amines sel
     664
     665> select clear
     666
     667> color C dodger blue
     668
     669> color Amines orchid
     670
     671> color F pale green
     672
     673> select clear
     674
     675> lighting soft
     676
     677> lighting shadows true intensity 0.5
     678
     679> graphics silhouettes false
     680
     681> graphics silhouettes true
     682
     683> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4F4 cavities_cav1.dx"
     684
     685Opened A4F4 cavities_cav1.dx as #2, grid size 97,103,99, pixel 0.2, shown at
     686level -6,6, step 1, values float32 
     687
     688> volume #2 color #dffb81 color #b2b2b2
     689
     690> volume #2 level 4.61 level 6
     691
     692> volume #2 level 1.282 level 6
     693
     694> volume #2 color #bad06b color #b2b2b2
     695
     696> volume #2 level 4.998 level 6
     697
     698> hide #1 models
     699
     700> volume #2 color #79834c58 color #b2b2b2
     701
     702> volume #2 color #79834cc0 color #b2b2b2
     703
     704> volume #2 color #a7b469c0 color #b2b2b2
     705
     706> volume #2 color #8ed243 color #b2b2b2
     707
     708> volume #2 color #8ed24390 color #b2b2b2
     709
     710> volume #2 color #ff9f3f color #b2b2b2
     711
     712> volume #2 color #ff9f3fe2 color #b2b2b2
     713
     714> volume #2 color #ff9f3f00 color #b2b2b2
     715
     716> volume #2 color #ff9f3f24 color #b2b2b2
     717
     718> volume #2 color #ffb04e color #b2b2b2
     719
     720> show #1 models
     721
     722> close session
     723
     724> open "/Users/tomkunde/Documents/Work/MOL-files Cages/Stacked FF24 .cxs"
     725> format session
     726
     727opened ChimeraX session 
     728
     729> open "/Users/tomkunde/Documents/Work/Crystal structures/FF24 H2
     730> cavity_cav1.dx"
     731
     732Opened FF24 H2 cavity_cav1.dx as #2, grid size 85,55,56, pixel 0.2, shown at
     733level -6,6, step 1, values float32 
     734
     735> volume #2 level 5 level 6
     736
     737> volume #2 color #e5371a color #ffffb2
     738
     739> volume #2 color #e54f52 color #ffffb2
     740
     741> volume #2 level 3 level 6
     742
     743> color #1 #1e90ff1e
     744
     745> style sphere
     746
     747Changed 396 atom styles 
     748
     749> undo
     750
     751> color Amines orchid
     752
     753Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
     754'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
     755or a keyword 
     756
     757> color DACH orchid
     758
     759> color F pale green
     760
     761> style sphere
     762
     763Changed 396 atom styles 
     764
     765> movie record
     766
     767> turn y 2 180
     768
     769> wait 180
     770
     771> movie encode /Users/tomkunde/Desktop/movie9.mp4
     772
     773Movie saved to /Users/tomkunde/Desktop/movie9.mp4 
     774 
     775
     776> close session
     777
     778> open "/Users/tomkunde/Documents/Work/Untitled Folder/2+2-PTO-
     779> MC_optimized.mol2"
     780
     781Opened 2+2-PTO-MC_optimized.mol2 containing 1 structures (104 atoms, 112
     782bonds) 
     783
     784> hide H
     785
     786Drag select of 6 atoms, 7 bonds 
     787
     788> name frozen DACH sel
     789
     790> color C doger blue
     791
     792Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
     793'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
     794or a keyword 
     795
     796> color C dodger blue
     797
     798> color F pale green
     799
     800> color DACH orchid
     801
     802> style sphere
     803
     804Changed 104 atom styles 
     805
     806> lighting simple
     807
     808> lighting soft
     809
     810> lighting shadows true intensity 0.5
     811
     812> graphics silhouettes false
     813
     814> graphics silhouettes true
     815
     816> select clear
     817
     818> save "/Users/tomkunde/Documents/Work/Untitled Folder/2+2 PTO-MC
     819> speheres.png" transparentBackground true
     820
     821> save "/Users/tomkunde/Documents/Work/Untitled Folder/2+2 PTO-MC.cxs"
     822
     823> close session
     824
     825> open "/Users/tomkunde/Documents/Work/Untitled Folder/3+3-PTO-
     826> MC_optimized.mol2"
     827
     828Opened 3+3-PTO-MC_optimized.mol2 containing 1 structures (156 atoms, 168
     829bonds) 
     830
     831> hdie H
     832
     833Unknown command: hdie H 
     834
     835> hide H
     836
     837Drag select of 6 atoms, 6 bonds 
     838Drag select of 6 atoms, 8 bonds 
     839
     840> name frozen DACH sel
     841
     842> style sphere
     843
     844Changed 156 atom styles 
     845
     846> color C dodger blue
     847
     848> color DACH orchid
     849
     850> color F pale green
     851
     852> show H
     853
     854> select clear
     855
     856> lighting soft
     857
     858> lighting shadows true intensity 0.5
     859
     860> graphics silhouettes false
     861
     862> graphics silhouettes true
     863
     864> save "/Users/tomkunde/Documents/Work/Untitled Folder/3+3 PTO-MC spheres.png"
     865> transparentBackground true
     866
     867> save "/Users/tomkunde/Documents/Work/Untitled Folder/3+3 PTO-MC.cxs"
     868
     869> close session
     870
     871> open "/Users/tomkunde/Documents/Work/Untitled Folder/4+4-PTO-
     872> MC_optimized.mol2"
     873
     874Opened 4+4-PTO-MC_optimized.mol2 containing 1 structures (208 atoms, 224
     875bonds) 
     876
     877> hdie H
     878
     879Unknown command: hdie H 
     880
     881> hide H
     882
     883Drag select of 6 atoms, 7 bonds 
     884Drag select of 6 atoms, 8 bonds 
     885Drag select of 6 atoms, 6 bonds 
     886
     887> name frozen DACH sel
     888
     889> color C dodger blue
     890
     891> color DACH orchid
     892
     893> color F pale green
     894
     895> show H
     896
     897> style sphere
     898
     899Changed 208 atom styles 
     900
     901> lighting soft
     902
     903> lighting shadows true intensity 0.5
     904
     905> select clear
     906
     907> save "/Users/tomkunde/Documents/Work/Untitled Folder/4+4 PTO-MC spheres.png"
     908> transparentBackground true
     909
     910> save "/Users/tomkunde/Documents/Work/Untitled Folder/4+4 PTO-MC.cxs"
     911
     912> open "/Users/tomkunde/Documents/Work/Untitled Folder/3+3 PTO-MC.cxs"
     913
     914opened ChimeraX session 
     915
     916> open "/Users/tomkunde/Documents/Work/Untitled Folder/4+4 PTO-MC.cxs"
     917
     918opened ChimeraX session 
     919
     920> open "/Users/tomkunde/Documents/Work/Untitled Folder/3+3-PTO-
     921> MC_optimized.mol2"
     922
     923Opened 3+3-PTO-MC_optimized.mol2 containing 1 structures (156 atoms, 168
     924bonds) 
     925
     926> open "/Users/tomkunde/Documents/Work/Untitled Folder/2+2-PTO-
     927> MC_optimized.mol2"
     928
     929Opened 2+2-PTO-MC_optimized.mol2 containing 1 structures (104 atoms, 112
     930bonds) 
     931
     932> select add #2
     933
     934156 atoms, 168 bonds, 1 residue, 1 model selected 
     935
     936> ui mousemode right "translate selected models"
     937
     938> view matrix models #2,1,0,0,-1.5242,0,1,0,0.22619,0,0,1,0.21368
     939
     940> select add #3
     941
     942260 atoms, 280 bonds, 2 residues, 2 models selected 
     943
     944> view matrix models
     945> #2,1,0,0,-2.996,0,1,0,2.1086,0,0,1,0.51162,#3,1,0,0,-1.4718,0,1,0,1.8824,0,0,1,0.29794
     946
     947> select subtract #2
     948
     949104 atoms, 112 bonds, 1 residue, 1 model selected 
     950
     951> view matrix models #3,1,0,0,-1.1602,0,1,0,1.4321,0,0,1,0.23202
     952
     953> select subtract #3
     954
     955Nothing selected 
     956
     957> select add #2
     958
     959156 atoms, 168 bonds, 1 residue, 1 model selected 
     960
     961> view matrix models #2,1,0,0,-0.62681,0,1,0,-1.0957,0,0,1,0.022435
     962
     963> ui mousemode right "rotate selected models"
     964
     965> view matrix models
     966> #2,0.99495,0.1002,0.0061834,-0.83994,-0.10028,0.99488,0.012957,-1.3562,-0.0048533,-0.013511,0.9999,0.036232
     967
     968> ui mousemode right "translate selected models"
     969
     970> view matrix models
     971> #2,0.99495,0.1002,0.0061834,-1.1189,-0.10028,0.99488,0.012957,-0.55543,-0.0048533,-0.013511,0.9999,0.11714
     972
     973> select subtract #2
     974
     975Nothing selected 
     976
     977> select add #3
     978
     979104 atoms, 112 bonds, 1 residue, 1 model selected 
     980
     981> ui mousemode right "rotate selected models"
     982
     983> view matrix models
     984> #3,0.97326,0.22718,0.033986,-1.1611,-0.2274,0.9738,0.0027125,1.3391,-0.032479,-0.010368,0.99942,0.21844
     985
     986> hide #1 models
     987
     988> view matrix models
     989> #3,0.9753,0.21348,0.056662,-1.2002,-0.21557,0.97591,0.033704,1.2946,-0.048102,-0.045086,0.99782,0.20578
     990
     991> view matrix models
     992> #3,-0.05356,0.98428,0.16831,-1.5335,-0.9981,-0.057892,0.020932,0.74892,0.030347,-0.16687,0.98551,0.21983
     993
     994> view matrix models
     995> #3,-0.047196,0.9978,0.046546,-1.3339,-0.99837,-0.048612,0.029766,0.73734,0.031964,-0.045065,0.99847,0.23345
     996
     997> ui mousemode right "translate selected models"
     998
     999> view matrix models
     1000> #3,-0.047196,0.9978,0.046546,-2.6652,-0.99837,-0.048612,0.029766,-0.080139,0.031964,-0.045065,0.99847,0.022365
     1001
     1002> view matrix models
     1003> #3,-0.047196,0.9978,0.046546,-1.2526,-0.99837,-0.048612,0.029766,-0.10783,0.031964,-0.045065,0.99847,-0.077005
     1004
     1005> style sticks
     1006
     1007Expected a keyword 
     1008
     1009> style stick
     1010
     1011Changed 468 atom styles 
     1012
     1013> show #1 models
     1014
     1015> hide #3 models
     1016
     1017> select subtract #3
     1018
     1019Nothing selected 
     1020
     1021> select add #2
     1022
     1023156 atoms, 168 bonds, 1 residue, 1 model selected 
     1024
     1025> view matrix models
     1026> #2,0.99495,0.1002,0.0061834,-0.30089,-0.10028,0.99488,0.012957,-0.70809,-0.0048533,-0.013511,0.9999,0.33853
     1027
     1028> select subtract #2
     1029
     1030Nothing selected 
     1031
     1032> show #3 models
     1033
     1034> color #1 #dffb81 transparency 0
     1035
     1036> color #1 #8ed243 transparency 0
     1037
     1038> color #2 #8ed243 transparency 0
     1039
     1040> color #2 #b4d28e transparency 0
     1041
     1042> color #2 #bad29a transparency 0
     1043
     1044> color #3 #8ed243 transparency 0
     1045
     1046> color #3 #d2d0c5 transparency 0
     1047
     1048> select add #2
     1049
     1050156 atoms, 168 bonds, 1 residue, 1 model selected 
     1051
     1052> view matrix models
     1053> #2,0.99495,0.1002,0.0061834,-0.70304,-0.10028,0.99488,0.012957,-0.99916,-0.0048533,-0.013511,0.9999,-8.5279
     1054
     1055> select subtract #2
     1056
     1057Nothing selected 
     1058
     1059> select add #3
     1060
     1061104 atoms, 112 bonds, 1 residue, 1 model selected 
     1062
     1063> view matrix models
     1064> #3,-0.047196,0.9978,0.046546,-2.1282,-0.99837,-0.048612,0.029766,-0.70898,0.031964,-0.045065,0.99847,-18.327
     1065
     1066> select subtract #3
     1067
     1068Nothing selected 
     1069
     1070> style sphere
     1071
     1072Changed 468 atom styles 
     1073
     1074> select add #3
     1075
     1076104 atoms, 112 bonds, 1 residue, 1 model selected 
     1077
     1078> view matrix models
     1079> #3,-0.047196,0.9978,0.046546,-2.4058,-0.99837,-0.048612,0.029766,-0.84975,0.031964,-0.045065,0.99847,-20.738
     1080
     1081> select subtract #3
     1082
     1083Nothing selected 
     1084
     1085> select add #2
     1086
     1087156 atoms, 168 bonds, 1 residue, 1 model selected 
     1088
     1089> view matrix models
     1090> #2,0.99495,0.1002,0.0061834,-1.0333,-0.10028,0.99488,0.012957,-1.0874,-0.0048533,-0.013511,0.9999,-10.862
     1091
     1092> view matrix models
     1093> #2,0.99495,0.1002,0.0061834,-1.9012,-0.10028,0.99488,0.012957,-0.47925,-0.0048533,-0.013511,0.9999,-11.345
     1094
     1095> select subtract #2
     1096
     1097Nothing selected 
     1098
     1099> select add #3
     1100
     1101104 atoms, 112 bonds, 1 residue, 1 model selected 
     1102
     1103> view matrix models
     1104> #3,-0.047196,0.9978,0.046546,-2.5378,-0.99837,-0.048612,0.029766,-0.83539,0.031964,-0.045065,0.99847,-21.337
     1105
     1106> ui mousemode right translate
     1107
     1108> select clear
     1109
     1110> save "/Users/tomkunde/Documents/Work/Untitled Folder/PTO-MC comparison
     1111> spheres side.png" transparentBackground true
     1112
     1113> ui mousemode right "translate selected models"
     1114
     1115> select add #3
     1116
     1117104 atoms, 112 bonds, 1 residue, 1 model selected 
     1118
     1119> view matrix models
     1120> #3,-0.047196,0.9978,0.046546,-3.7209,-0.99837,-0.048612,0.029766,-0.89114,0.031964,-0.045065,0.99847,-21.222
     1121
     1122> ui mousemode right "rotate selected models"
     1123
     1124> select subtract #3
     1125
     1126Nothing selected 
     1127
     1128> select add #2
     1129
     1130156 atoms, 168 bonds, 1 residue, 1 model selected 
     1131
     1132> view matrix models
     1133> #2,0.98411,0.17751,0.0036814,-2.0689,-0.17755,0.98391,0.020004,-0.65197,-7.1303e-05,-0.02034,0.99979,-11.321
     1134
     1135> select subtract #2
     1136
     1137Nothing selected 
     1138
     1139> ui mousemode right translate
     1140
     1141> save "/Users/tomkunde/Documents/Work/Untitled Folder/Comparison PTO-MC
     1142> spheres back view.png" transparentBackground true
     1143
     1144> style ball
     1145
     1146Changed 468 atom styles 
     1147
     1148> select add #1
     1149
     1150208 atoms, 224 bonds, 1 residue, 1 model selected 
     1151
     1152> ui mousemode right "translate selected models"
     1153
     1154> view matrix models #1,1,0,0,-1.6214,0,1,0,-0.034575,0,0,1,-0.039284
     1155
     1156> select subtract #1
     1157
     1158Nothing selected 
     1159
     1160> save "/Users/tomkunde/Documents/Work/Untitled Folder/Comparison PTO-MC
     1161> sideview balls.png" transparentBackground true
     1162
     1163> movie record
     1164
     1165> turn y 2 180
     1166
     1167> wait 180
     1168
     1169> movie encode /Users/tomkunde/Desktop/movie10.mp4
     1170
     1171Movie saved to /Users/tomkunde/Desktop/movie10.mp4 
     1172 
     1173
     1174> style sphere
     1175
     1176Changed 468 atom styles 
     1177
     1178> movie record
     1179
     1180> turn y 2 180
     1181
     1182> wait 180
     1183
     1184> movie encode /Users/tomkunde/Desktop/movie11.mp4
     1185
     1186Movie saved to /Users/tomkunde/Desktop/movie11.mp4 
     1187 
     1188
     1189> open "/Users/tomkunde/Documents/Work/Untitled
     1190> Folder/PTOnew2+3cage_optimized.mol2"
     1191
     1192Opened PTOnew2+3cage_optimized.mol2 containing 1 structures (180 atoms, 192
     1193bonds) 
     1194
     1195> close session
     1196
     1197> open "/Users/tomkunde/Documents/Work/Untitled
     1198> Folder/PTOnew2+3cage_optimized.mol2" format mol2
     1199
     1200Opened PTOnew2+3cage_optimized.mol2 containing 1 structures (180 atoms, 192
     1201bonds) 
     1202
     1203> hide H
     1204
     1205Drag select of 15 atoms, 17 bonds 
     1206
     1207> close session
     1208
     1209> open "/Users/tomkunde/Documents/Work/Untitled
     1210> Folder/PTOnew2+3cage_optimized.mol2"
     1211
     1212Opened PTOnew2+3cage_optimized.mol2 containing 1 structures (180 atoms, 192
     1213bonds) 
     1214
     1215> hide H
     1216
     1217Drag select of 15 atoms, 17 bonds 
     1218
     1219> name frozen Amines sel
     1220
     1221> color C dodger blue
     1222
     1223> color Amines orchid
     1224
     1225> color F pale green
     1226
     1227> style sphere
     1228
     1229Changed 180 atom styles 
     1230
     1231> lighting soft
     1232
     1233> lighting shadows true intensity 0.5
     1234
     1235> select clear
     1236
     1237> style ball
     1238
     1239Changed 180 atom styles 
     1240
     1241> open "/Users/tomkunde/Documents/Work/Untitled Folder/PTOne2+3
     1242> cavity_cav1.dx"
     1243
     1244Opened PTOne2+3 cavity_cav1.dx as #2, grid size 61,55,68, pixel 0.2, shown at
     1245level -6,6, step 1, values float32 
     1246
     1247> volume #2 level 3 level 6
     1248
     1249> volume #2 color #8ed243 color #b2ffff
     1250
     1251> volume #2 color #ff9f3f color #b2ffff
     1252
     1253> style sphere
     1254
     1255Changed 180 atom styles 
     1256
     1257> color #1 #1e90ff74
     1258
     1259> color #1 #1e90ff50
     1260
     1261> color #1 #1e90ff43
     1262
     1263> color C dodger blue
     1264
     1265> color Amines orchid
     1266
     1267> color F pale green
     1268
     1269> movie record
     1270
     1271> turn y 2 180
     1272
     1273> wait 180
     1274
     1275> movie encode /Users/tomkunde/Desktop/movie12.mp4
     1276
     1277Movie saved to /Users/tomkunde/Desktop/movie12.mp4 
     1278 
     1279
     1280> show H
     1281
     1282> Color H white
     1283
     1284Unknown command: Color H white 
     1285
     1286> color H white
     1287
     1288> graphics silhouettes false
     1289
     1290> graphics silhouettes true
     1291
     1292> graphics silhouettes false
     1293
     1294> graphics silhouettes true
     1295
     1296> graphics silhouettes false
     1297
     1298> graphics silhouettes true
     1299
     1300> volume #2 level 5 level 6
     1301
     1302> close session
     1303
     1304> open "/Users/tomkunde/Documents/Work/Untitled
     1305> Folder/PTOnew2+3cage_optimized.mol2" format mol2
     1306
     1307No such file/path: /Users/tomkunde/Documents/Work/Untitled
     1308Folder/PTOnew2+3cage_optimized.mol2 
     1309
     1310> open "/Users/tomkunde/Documents/Work/Jupyter
     1311> Notebooks/PTOnew2+3cage_optimized.mol2"
     1312
     1313Opened PTOnew2+3cage_optimized.mol2 containing 1 structures (180 atoms, 192
     1314bonds) 
     1315
     1316> open "/Users/tomkunde/Documents/Work/Jupyter Notebooks/PTOne2+3
     1317> cavity_cav1.dx"
     1318
     1319Opened PTOne2+3 cavity_cav1.dx as #2, grid size 61,55,68, pixel 0.2, shown at
     1320level -6,6, step 1, values float32 
     1321
     1322> volume #2 level 3 level 6
     1323
     1324> volume #2 level 5 level 6
     1325
     1326> volume #2 level 3 level 6
     1327
     1328> open "/Users/tomkunde/Documents/Work/Jupyter
     1329> Notebooks/GC1TREN_optimized.mol2"
     1330
     1331Opened GC1TREN_optimized.mol2 containing 1 structures (268 atoms, 288 bonds) 
     1332
     1333> close session
     1334
     1335> open "/Users/tomkunde/Documents/Work/Jupyter
     1336> Notebooks/GC1TREN_optimized.mol2"
     1337
     1338Opened GC1TREN_optimized.mol2 containing 1 structures (268 atoms, 288 bonds) 
     1339
     1340> hide H
     1341
     1342> style ball
     1343
     1344Changed 268 atom styles 
     1345Drag select of 1 atoms 
     1346Drag select of 1 atoms, 1 bonds 
     1347Drag select of 1 atoms 
     1348Drag select of 2 atoms, 1 bonds 
     1349Drag select of 2 atoms, 2 bonds 
     1350Drag select of 3 atoms, 2 bonds 
     1351Drag select of 2 atoms, 1 bonds 
     1352
     1353> select add /?:1@@serial_number=-1
     1354
     1355268 atoms, 288 bonds, 1 residue, 1 model selected 
     1356
     1357> undo
     1358
     1359Drag select of 1 atoms 
     1360Drag select of 1 atoms, 1 bonds 
     1361Drag select of 1 atoms 
     1362Drag select of 2 atoms, 2 bonds 
     1363
     1364> name frozen TREN sel
     1365
     1366> color C dodger blue
     1367
     1368> color TREN orchid
     1369
     1370> color F pale green
     1371
     1372> select clear
     1373
     1374> lighting soft
     1375
     1376> lighting shadows true intensity 0.5
     1377
     1378> graphics silhouettes false
     1379
     1380> graphics silhouettes true
     1381
     1382> ui mousemode right "translate selected models"
     1383
     1384> ui mousemode right zoom
     1385
     1386> style sphere
     1387
     1388Changed 268 atom styles 
     1389
     1390> open "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1TREN
     1391> Cavity_cav1.dx"
     1392
     1393Opened GC1TREN Cavity_cav1.dx as #2, grid size 89,83,89, pixel 0.2, shown at
     1394level -6,6, step 1, values float32 
     1395
     1396> volume #2 level 3 level 6
     1397
     1398> style stick
     1399
     1400Changed 268 atom styles 
     1401
     1402> volume #2 color #ff9f3f color #ffb2ff
     1403
     1404> save "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1TREN w Cavity.cxs"
     1405
     1406> close session
     1407
     1408> open "/Users/tomkunde/Documents/Work/Jupyter
     1409> Notebooks/GC1_A4H4_optimized.mol2"
     1410
     1411Opened GC1_A4H4_optimized.mol2 containing 1 structures (268 atoms, 288 bonds) 
     1412
     1413> hide H
     1414
     1415> style ball
     1416
     1417Changed 268 atom styles 
     1418Drag select of 2 atoms, 1 bonds 
     1419Drag select of 2 atoms, 3 bonds 
     1420Drag select of 2 atoms, 2 bonds 
     1421Drag select of 2 atoms, 3 bonds 
     1422Drag select of 1 atoms, 2 bonds 
     1423Drag select of 2 atoms, 2 bonds 
     1424Drag select of 1 atoms 
     1425Drag select of 2 atoms, 2 bonds 
     1426Drag select of 2 atoms, 1 bonds 
     1427Drag select of 2 atoms, 2 bonds 
     1428
     1429> name frozen TREN sel
     1430
     1431> color C orange
     1432
     1433> color TREN orchid
     1434
     1435> lighting soft
     1436
     1437> lighting shadows true intensity 0.5
     1438
     1439> graphics silhouettes false
     1440
     1441> graphics silhouettes true
     1442
     1443> select /?:1@@serial_number=-1
     1444
     1445268 atoms, 288 bonds, 1 residue, 1 model selected 
     1446
     1447> select clear
     1448
     1449> open "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1 A4H4_cav1.dx"
     1450
     1451Opened GC1 A4H4_cav1.dx as #2, grid size 88,86,86, pixel 0.2, shown at level
     1452-6,6, step 1, values float32 
     1453
     1454> volume #2 level 3 level 6
     1455
     1456> volume #2 color #ff9f3f color #ffb2b2
     1457
     1458> volume #2 color #8ed243 color #ffb2b2
     1459
     1460> save "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1A4H4 w cavity.cxs"
     1461
     1462> close session
     1463
     1464> open "/Users/tomkunde/Documents/Work/Jupyter
     1465> Notebooks/GC1_A4H3F1_optimized.mol2"
     1466
     1467Opened GC1_A4H3F1_optimized.mol2 containing 1 structures (268 atoms, 288
     1468bonds) 
     1469
     1470> hide H
     1471
     1472> style ball
     1473
     1474Changed 268 atom styles 
     1475Drag select of 2 atoms, 1 bonds 
     1476Drag select of 1 atoms 
     1477Drag select of 1 atoms, 1 bonds 
     1478Drag select of 2 atoms, 1 bonds 
     1479Drag select of 2 atoms, 2 bonds 
     1480Drag select of 2 atoms, 1 bonds 
     1481Drag select of 1 atoms 
     1482
     1483> name frozen TREN sel
     1484
     1485> select clear
     1486
     1487Drag select of 2 atoms, 4 bonds 
     1488Drag select of 1 atoms, 1 bonds 
     1489Drag select of 1 atoms 
     1490Drag select of 1 atoms, 1 bonds 
     1491Drag select of 1 atoms 
     1492Drag select of 3 atoms, 3 bonds 
     1493Drag select of 3 atoms, 2 bonds 
     1494Drag select of 2 atoms, 4 bonds 
     1495Drag select of 1 atoms 
     1496Drag select of 1 atoms, 2 bonds 
     1497Drag select of 1 atoms 
     1498Drag select of 2 atoms, 1 bonds 
     1499Drag select of 1 atoms 
     1500Drag select of 1 atoms, 1 bonds 
     1501Drag select of 1 atoms, 2 bonds 
     1502Drag select of 2 atoms, 1 bonds 
     1503Drag select of 1 atoms, 2 bonds 
     1504
     1505> name frozen F-Aldehyde sel
     1506
     1507> color C orange
     1508
     1509> color TREN orchid
     1510
     1511> color F-Aldehyde dodger blue
     1512
     1513> color F pale green
     1514
     1515> lighting soft
     1516
     1517> lighting shadows true intensity 0.5
     1518
     1519> select clear
     1520
     1521> open "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1A4H3F1
     1522> cavity_cav1.dx"
     1523
     1524Opened GC1A4H3F1 cavity_cav1.dx as #2, grid size 92,85,90, pixel 0.2, shown at
     1525level -6,6, step 1, values float32 
     1526
     1527> volume #2 level 3 level 6
     1528
     1529> volume #2 color #8ed243 color #b2ffb2
     1530
     1531> save "/Users/tomkunde/Documents/Work/Jupyter Notebooks/GC1A4H3F1 w
     1532> cavity.cxs"
     1533
     1534> close session
     1535
     1536> open "/Users/tomkunde/Documents/Work/Jupyter
     1537> Notebooks/GC1_A4H2F2_optimized.mol2"
     1538
     1539Opened GC1_A4H2F2_optimized.mol2 containing 1 structures (268 atoms, 288
     1540bonds) 
     1541
     1542> style sphere
     1543
     1544Changed 268 atom styles 
     1545
     1546> close session
     1547
     1548> open "/Users/tomkunde/Documents/Work/Untitled Folder/GC2_optimized.mol"
     1549> format sdf
     1550
     1551No such file/path: /Users/tomkunde/Documents/Work/Untitled
     1552Folder/GC2_optimized.mol 
     1553
     1554> open "/Users/tomkunde/Documents/Work/MOL-files Cages/Kwano Cage colored.cxs"
     1555> format session
     1556
     1557opened ChimeraX session 
     1558
     1559> style sphere
     1560
     1561Changed 345 atom styles 
     1562
     1563> close session
     1564
     1565> open "/Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3.cxs" format
     1566> session
     1567
     1568No such file/path: /Users/tomkunde/Documents/Work/Untitled Folder/A4H1F3.cxs 
     1569
     1570
     1571===== Log before crash end =====
     1572
     1573Log:
     1574UCSF ChimeraX version: 1.4 (2022-06-03) 
     1575© 2016-2022 Regents of the University of California. All rights reserved. 
     1576How to cite UCSF ChimeraX 
     1577
     1578
     1579
     1580
     1581OpenGL version: 4.1 Metal - 76.3
     1582OpenGL renderer: Apple M1
     1583OpenGL vendor: Apple
     1584
     1585Python: 3.9.11
     1586Locale: UTF-8
     1587Qt version: PyQt6 6.3.0, Qt 6.3.0
     1588Qt runtime version: 6.3.0
     1589Qt platform: cocoa
     1590Hardware:
     1591
     1592    Hardware Overview:
     1593
     1594      Model Name: MacBook Pro
     1595      Model Identifier: MacBookPro17,1
     1596      Processor Name: Unknown
     1597      Processor Speed: 2,4 GHz
     1598      Number of Processors: 1
     1599      Total Number of Cores: 8
     1600      L2 Cache: 8 MB
     1601      Memory: 16 GB
     1602
     1603Software:
     1604
     1605    System Software Overview:
     1606
     1607      System Version: macOS 12.4 (21F79)
     1608      Kernel Version: Darwin 21.5.0
     1609      Time since boot: 33 days 3:28
     1610
     1611Graphics/Displays:
     1612
     1613    Apple M1:
     1614
     1615      Chipset Model: Apple M1
     1616      Type: GPU
     1617      Bus: Built-In
     1618      Total Number of Cores: 8
     1619      Vendor: Apple (0x106b)
     1620      Metal Family: Supported, Metal GPUFamily Apple 7
     1621      Displays:
     1622        Color LCD:
     1623          Display Type: Built-In Retina LCD
     1624          Resolution: 2560 x 1600 Retina
     1625          Main Display: Yes
     1626          Mirror: Off
     1627          Online: Yes
     1628          Automatically Adjust Brightness: Yes
     1629          Connection Type: Internal
     1630        HP 27fh:
     1631          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
     1632          UI Looks like: 1920 x 1080 @ 60.00Hz
     1633          Mirror: Off
     1634          Online: Yes
     1635
     1636
     1637Installed Packages:
     1638    alabaster: 0.7.12
     1639    appdirs: 1.4.4
     1640    appnope: 0.1.3
     1641    Babel: 2.10.1
     1642    backcall: 0.2.0
     1643    blockdiag: 3.0.0
     1644    certifi: 2021.10.8
     1645    cftime: 1.6.0
     1646    charset-normalizer: 2.0.12
     1647    ChimeraX-AddCharge: 1.2.3
     1648    ChimeraX-AddH: 2.1.11
     1649    ChimeraX-AlignmentAlgorithms: 2.0
     1650    ChimeraX-AlignmentHdrs: 3.2.1
     1651    ChimeraX-AlignmentMatrices: 2.0
     1652    ChimeraX-Alignments: 2.4.3
     1653    ChimeraX-AlphaFold: 1.0
     1654    ChimeraX-AltlocExplorer: 1.0.2
     1655    ChimeraX-AmberInfo: 1.0
     1656    ChimeraX-Arrays: 1.0
     1657    ChimeraX-Atomic: 1.39.1
     1658    ChimeraX-AtomicLibrary: 7.0
     1659    ChimeraX-AtomSearch: 2.0.1
     1660    ChimeraX-AxesPlanes: 2.1
     1661    ChimeraX-BasicActions: 1.1
     1662    ChimeraX-BILD: 1.0
     1663    ChimeraX-BlastProtein: 2.1.1
     1664    ChimeraX-BondRot: 2.0
     1665    ChimeraX-BugReporter: 1.0
     1666    ChimeraX-BuildStructure: 2.7
     1667    ChimeraX-Bumps: 1.0
     1668    ChimeraX-BundleBuilder: 1.1
     1669    ChimeraX-ButtonPanel: 1.0
     1670    ChimeraX-CageBuilder: 1.0
     1671    ChimeraX-CellPack: 1.0
     1672    ChimeraX-Centroids: 1.2
     1673    ChimeraX-ChemGroup: 2.0
     1674    ChimeraX-Clashes: 2.2.4
     1675    ChimeraX-ColorActions: 1.0
     1676    ChimeraX-ColorGlobe: 1.0
     1677    ChimeraX-ColorKey: 1.5.1
     1678    ChimeraX-CommandLine: 1.2.3
     1679    ChimeraX-ConnectStructure: 2.0.1
     1680    ChimeraX-Contacts: 1.0
     1681    ChimeraX-Core: 1.4
     1682    ChimeraX-CoreFormats: 1.1
     1683    ChimeraX-coulombic: 1.3.2
     1684    ChimeraX-Crosslinks: 1.0
     1685    ChimeraX-Crystal: 1.0
     1686    ChimeraX-CrystalContacts: 1.0
     1687    ChimeraX-DataFormats: 1.2.2
     1688    ChimeraX-Dicom: 1.1
     1689    ChimeraX-DistMonitor: 1.1.5
     1690    ChimeraX-Dssp: 2.0
     1691    ChimeraX-EMDB-SFF: 1.0
     1692    ChimeraX-ExperimentalCommands: 1.0
     1693    ChimeraX-FileHistory: 1.0
     1694    ChimeraX-FunctionKey: 1.0
     1695    ChimeraX-Geometry: 1.2
     1696    ChimeraX-gltf: 1.0
     1697    ChimeraX-Graphics: 1.1
     1698    ChimeraX-Hbonds: 2.1.2
     1699    ChimeraX-Help: 1.2
     1700    ChimeraX-HKCage: 1.3
     1701    ChimeraX-IHM: 1.1
     1702    ChimeraX-ImageFormats: 1.2
     1703    ChimeraX-IMOD: 1.0
     1704    ChimeraX-IO: 1.0.1
     1705    ChimeraX-ItemsInspection: 1.0
     1706    ChimeraX-Label: 1.1.1
     1707    ChimeraX-ListInfo: 1.1.1
     1708    ChimeraX-Log: 1.1.5
     1709    ChimeraX-LookingGlass: 1.1
     1710    ChimeraX-Maestro: 1.8.1
     1711    ChimeraX-Map: 1.1
     1712    ChimeraX-MapData: 2.0
     1713    ChimeraX-MapEraser: 1.0
     1714    ChimeraX-MapFilter: 2.0
     1715    ChimeraX-MapFit: 2.0
     1716    ChimeraX-MapSeries: 2.1
     1717    ChimeraX-Markers: 1.0
     1718    ChimeraX-Mask: 1.0
     1719    ChimeraX-MatchMaker: 2.0.6
     1720    ChimeraX-MDcrds: 2.6
     1721    ChimeraX-MedicalToolbar: 1.0.1
     1722    ChimeraX-Meeting: 1.0
     1723    ChimeraX-MLP: 1.1
     1724    ChimeraX-mmCIF: 2.7
     1725    ChimeraX-MMTF: 2.1
     1726    ChimeraX-Modeller: 1.5.5
     1727    ChimeraX-ModelPanel: 1.3.2
     1728    ChimeraX-ModelSeries: 1.0
     1729    ChimeraX-Mol2: 2.0
     1730    ChimeraX-Morph: 1.0
     1731    ChimeraX-MouseModes: 1.1
     1732    ChimeraX-Movie: 1.0
     1733    ChimeraX-Neuron: 1.0
     1734    ChimeraX-Nucleotides: 2.0.2
     1735    ChimeraX-OpenCommand: 1.9
     1736    ChimeraX-PDB: 2.6.6
     1737    ChimeraX-PDBBio: 1.0
     1738    ChimeraX-PDBLibrary: 1.0.2
     1739    ChimeraX-PDBMatrices: 1.0
     1740    ChimeraX-PickBlobs: 1.0
     1741    ChimeraX-Positions: 1.0
     1742    ChimeraX-PresetMgr: 1.1
     1743    ChimeraX-PubChem: 2.1
     1744    ChimeraX-ReadPbonds: 1.0.1
     1745    ChimeraX-Registration: 1.1
     1746    ChimeraX-RemoteControl: 1.0
     1747    ChimeraX-ResidueFit: 1.0
     1748    ChimeraX-RestServer: 1.1
     1749    ChimeraX-RNALayout: 1.0
     1750    ChimeraX-RotamerLibMgr: 2.0.1
     1751    ChimeraX-RotamerLibsDunbrack: 2.0
     1752    ChimeraX-RotamerLibsDynameomics: 2.0
     1753    ChimeraX-RotamerLibsRichardson: 2.0
     1754    ChimeraX-SaveCommand: 1.5.1
     1755    ChimeraX-SchemeMgr: 1.0
     1756    ChimeraX-SDF: 2.0
     1757    ChimeraX-Segger: 1.0
     1758    ChimeraX-Segment: 1.0
     1759    ChimeraX-SelInspector: 1.0
     1760    ChimeraX-SeqView: 2.6
     1761    ChimeraX-Shape: 1.0.1
     1762    ChimeraX-Shell: 1.0
     1763    ChimeraX-Shortcuts: 1.1
     1764    ChimeraX-ShowAttr: 1.0
     1765    ChimeraX-ShowSequences: 1.0
     1766    ChimeraX-SideView: 1.0
     1767    ChimeraX-Smiles: 2.1
     1768    ChimeraX-SmoothLines: 1.0
     1769    ChimeraX-SpaceNavigator: 1.0
     1770    ChimeraX-StdCommands: 1.8
     1771    ChimeraX-STL: 1.0
     1772    ChimeraX-Storm: 1.0
     1773    ChimeraX-StructMeasure: 1.0.1
     1774    ChimeraX-Struts: 1.0.1
     1775    ChimeraX-Surface: 1.0
     1776    ChimeraX-SwapAA: 2.0
     1777    ChimeraX-SwapRes: 2.1.1
     1778    ChimeraX-TapeMeasure: 1.0
     1779    ChimeraX-Test: 1.0
     1780    ChimeraX-Toolbar: 1.1.1
     1781    ChimeraX-ToolshedUtils: 1.2.1
     1782    ChimeraX-Tug: 1.0
     1783    ChimeraX-UI: 1.18.3
     1784    ChimeraX-uniprot: 2.2
     1785    ChimeraX-UnitCell: 1.0
     1786    ChimeraX-ViewDockX: 1.1.2
     1787    ChimeraX-VIPERdb: 1.0
     1788    ChimeraX-Vive: 1.1
     1789    ChimeraX-VolumeMenu: 1.0
     1790    ChimeraX-VTK: 1.0
     1791    ChimeraX-WavefrontOBJ: 1.0
     1792    ChimeraX-WebCam: 1.0
     1793    ChimeraX-WebServices: 1.1.0
     1794    ChimeraX-Zone: 1.0
     1795    colorama: 0.4.4
     1796    cxservices: 1.2
     1797    cycler: 0.11.0
     1798    Cython: 0.29.26
     1799    debugpy: 1.6.0
     1800    decorator: 5.1.1
     1801    docutils: 0.17.1
     1802    entrypoints: 0.4
     1803    filelock: 3.4.2
     1804    fonttools: 4.33.3
     1805    funcparserlib: 1.0.0
     1806    grako: 3.16.5
     1807    h5py: 3.7.0
     1808    html2text: 2020.1.16
     1809    idna: 3.3
     1810    ihm: 0.27
     1811    imagecodecs: 2021.11.20
     1812    imagesize: 1.3.0
     1813    ipykernel: 6.6.1
     1814    ipython: 7.31.1
     1815    ipython-genutils: 0.2.0
     1816    jedi: 0.18.1
     1817    Jinja2: 3.0.3
     1818    jupyter-client: 7.1.0
     1819    jupyter-core: 4.10.0
     1820    kiwisolver: 1.4.2
     1821    line-profiler: 3.4.0
     1822    lxml: 4.7.1
     1823    lz4: 3.1.10
     1824    MarkupSafe: 2.1.1
     1825    matplotlib: 3.5.1
     1826    matplotlib-inline: 0.1.3
     1827    msgpack: 1.0.3
     1828    nest-asyncio: 1.5.5
     1829    netCDF4: 1.5.8
     1830    networkx: 2.6.3
     1831    numexpr: 2.8.1
     1832    numpy: 1.22.1
     1833    openvr: 1.16.802
     1834    packaging: 21.0
     1835    ParmEd: 3.4.3
     1836    parso: 0.8.3
     1837    pexpect: 4.8.0
     1838    pickleshare: 0.7.5
     1839    Pillow: 9.0.1
     1840    pip: 21.3.1
     1841    pkginfo: 1.8.2
     1842    prompt-toolkit: 3.0.29
     1843    psutil: 5.9.0
     1844    ptyprocess: 0.7.0
     1845    pycollada: 0.7.2
     1846    pydicom: 2.2.2
     1847    Pygments: 2.11.2
     1848    PyOpenGL: 3.1.5
     1849    PyOpenGL-accelerate: 3.1.5
     1850    pyparsing: 3.0.9
     1851    PyQt6-commercial: 6.3.0
     1852    PyQt6-Qt6: 6.3.0
     1853    PyQt6-sip: 13.3.1
     1854    PyQt6-WebEngine-commercial: 6.3.0
     1855    PyQt6-WebEngine-Qt6: 6.3.0
     1856    python-dateutil: 2.8.2
     1857    pytz: 2022.1
     1858    pyzmq: 23.1.0
     1859    qtconsole: 5.3.0
     1860    QtPy: 2.1.0
     1861    RandomWords: 0.3.0
     1862    requests: 2.27.1
     1863    scipy: 1.7.3
     1864    setuptools: 59.8.0
     1865    sfftk-rw: 0.7.2
     1866    six: 1.16.0
     1867    snowballstemmer: 2.2.0
     1868    sortedcontainers: 2.4.0
     1869    Sphinx: 4.3.2
     1870    sphinx-autodoc-typehints: 1.15.2
     1871    sphinxcontrib-applehelp: 1.0.2
     1872    sphinxcontrib-blockdiag: 3.0.0
     1873    sphinxcontrib-devhelp: 1.0.2
     1874    sphinxcontrib-htmlhelp: 2.0.0
     1875    sphinxcontrib-jsmath: 1.0.1
     1876    sphinxcontrib-qthelp: 1.0.3
     1877    sphinxcontrib-serializinghtml: 1.1.5
     1878    suds-community: 1.0.0
     1879    tables: 3.7.0
     1880    tifffile: 2021.11.2
     1881    tinyarray: 1.2.4
     1882    tornado: 6.1
     1883    traitlets: 5.1.1
     1884    urllib3: 1.26.9
     1885    wcwidth: 0.2.5
     1886    webcolors: 1.11.1
     1887    wheel: 0.37.1
     1888    wheel-filename: 1.3.0
     1889
     1890}}}