Opened 8 months ago

Last modified 7 months ago

#17082 closed defect

Crash on Mac waking from sleep — at Version 1

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

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00000003c5f53000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000321c3b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000315437000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031442b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031341f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000312413000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000311407000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003103fb000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030f3ef000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030e3e3000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030d3d7000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030c3cb000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x000000020954c840 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.atom_search.ast (total: 66)


{"app_name":"ChimeraX","timestamp":"2025-03-12 17:18:28.00 -0500","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.3.1 (24D70)","roots_installed":0,"name":"ChimeraX","incident_id":"C95C91A0-634C-4FA8-B479-C6A82F46BE5A"}
{
  "uptime" : 320000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac14,7",
  "coalitionID" : 1298,
  "osVersion" : {
    "train" : "macOS 15.3.1",
    "build" : "24D70",
    "releaseType" : "User"
  },
  "captureTime" : "2025-03-12 17:15:03.0095 -0500",
  "codeSigningMonitor" : 1,
  "incident" : "C95C91A0-634C-4FA8-B479-C6A82F46BE5A",
  "pid" : 36381,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-03-10 10:40:07.2798 -0500",
  "procStartAbsTime" : 6220669938932,
  "procExitAbsTime" : 7871351155108,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"039446C8-56F1-54A1-9531-85BD2E8F600D","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "3C03AB57-DF91-6538-731F-87145E7E925C",
  "lowPowerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "740CAC07-7A35-4E6E-9C78-D586F3D0754E",
  "wakeTime" : 10492,
  "sleepWakeUUID" : "3D768235-8921-49C6-B635-202E4B6428D2",
  "sip" : "enabled",
  "vmRegionInfo" : "0x3463dd4c02c8 is not in any region.  Bytes after previous region: 57122482815689  Bytes before following region: 47949597113656\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x00003463dd4c02c8","rawCodes":[1,57603519152840],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00003463dd4c02c8"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":36381},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0x3463dd4c02c8 is not in any region.  Bytes after previous region: 57122482815689  Bytes before following region: 47949597113656\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] 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" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":5100632728},{"value":99},{"value":100},{"value":14432},{"value":0},{"value":4924532482374262097},{"value":4924532473932453137},{"value":14757395258967641293},{"value":4294967286},{"value":5100632658},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8887263936},{"value":0},{"value":11},{"value":259},{"value":8746486048,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":4389078576,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8709476352,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":8709476352,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTableView._rowSizeStyle"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6974979952},"cpsr":{"value":1073745920},"fp":{"value":5100632800},"sp":{"value":5100632768},"esr":{"value":1442840704,"description":" Address size 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fault"},"pc":{"value":6974713684},"far":{"value":0}},"frames":[{"imageOffset":3924,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":165},{"imageOffset":79364,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":165},{"imageOffset":39672,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":165},{"imageOffset":4764,"symbol":"mach_msg","symbolLocation":24,"imageIndex":165},{"imageOffset":66741424,"imageIndex":56},{"imageOffset":66197236,"imageIndex":56},{"imageOffset":66429892,"imageIndex":56},{"imageOffset":66432404,"imageIndex":56},{"imageOffset":66431884,"imageIndex":56},{"imageOffset":66431792,"imageIndex":56},{"imageOffset":66589352,"imageIndex":56},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":166},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":166}]},{"id":5549621,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":166}],"threadState":{"x":[{"value":13670264832},{"value":242563},{"value":13669728256},{"value":13670263680},{"value":7159812},{"value":1},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":13670263664},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6974959848},"far":{"value":0}}}],
  "usedImages" : [
[deleted to fit within ticket limits]
],
  "sharedCache" : {
  "base" : 6970474496,
  "size" : 4865835008,
  "uuid" : "d272b91e-f9f0-3854-b5b9-508b21c25dcc"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=204.6G written=103.9M(0%) resident=103.9M(0%) swapped_out=0K(0%) unallocated=204.5G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG image                          1712K       57 \nColorSync                          736K       38 \nCoreAnimation                     4752K      242 \nCoreGraphics                       112K        6 \nCoreGraphics (reserved)             16K        1         reserved VM address space (unallocated)\nCoreServices                       624K        2 \nCoreUI image data                 4992K       37 \nFoundation                          32K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                           203.3G      616 \nMALLOC guard page                  288K       18 \nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        896K       56 \nStack                            373.4M       57 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      564.1M      670 \nVM_ALLOCATE (reserved)           128.0M        1         reserved VM address space (unallocated)\n__AUTH                            5289K      673 \n__AUTH_CONST                      70.9M      921 \n__CTF                               824        1 \n__DATA                            33.6M     1077 \n__DATA_CONST                      34.3M     1093 \n__DATA_DIRTY                      2763K      342 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       638.3M      166 \n__OBJC_RW                         2374K        1 \n__TEXT                             1.3G     1113 \n__TPRO_CONST                       272K        2 \ndyld private memory                288K        3 \nmapped file                      580.7M      107 \nowned unmapped memory            130.7M        1 \npage table in kernel             103.9M        1 \nshared memory                     3200K       26 \n===========                     =======  ======= \nTOTAL                            207.2G     7347 \nTOTAL, minus reserved VM space   207.1G     7347 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "f0bf5ea4982ac5851c397249dd5d2858a627cfdc",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "6425c75e4327780c10cc4252",
      "factorPackIds" : {
        "SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE" : "642600a457e7664b1698eb32"
      },
      "deploymentId" : 240000004
    },
    {
      "rolloutId" : "63508950b3714d3622fc77f7",
      "factorPackIds" : {
        "SIRI_MEMORY_SYNC_CONFIG" : "6526e111d0c9ce2f459b54a8"
      },
      "deploymentId" : 240000015
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  "experiments" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/kompa012/Desktop/New Folder/Experiment6.mrc" format mrc

Opened Experiment6.mrc as #1, grid size 336,336,336, pixel 0.66, shown at
level 1.18, step 2, values float32  

> close

> toolshed show

> ui tool show Rotamers

Populating font family aliases took 164 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.  

> open 1TUP fromDatabase pdb format mmcif

Summary of feedback from opening 1TUP fetched from pdb  
---  
note | Fetching compressed mmCIF 1tup from http://files.rcsb.org/download/1tup.cif  
  
1tup title:  
Tumor suppressor P53 complexed with DNA [more info...]  
  
Chain information for 1tup #1  
---  
Chain | Description | UniProt  
A B C | PROTEIN (P53 TUMOR SUPPRESSOR ) | P53_HUMAN 94-312  
E | DNA (5'-D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3') |   
F | DNA (5'-D(*AP*TP*AP*AP*TP*TP*GP*GP*GP*CP*AP*AP*GP*TP*CP*TP*A P*GP*GP*AP*A)-3') |   
  
Non-standard residues in 1tup #1  
---  
ZN — zinc ion  
  

> open 1TSR fromDatabase pdb format mmcif

Summary of feedback from opening 1TSR fetched from pdb  
---  
note | Fetching compressed mmCIF 1tsr from http://files.rcsb.org/download/1tsr.cif  
  
1tsr title:  
P53 core domain In complex with DNA [more info...]  
  
Chain information for 1tsr #2  
---  
Chain | Description | UniProt  
A B C | PROTEIN (P53 TUMOR SUPPRESSOR) | P53_HUMAN 94-312  
E | DNA (5'-D(*TP*TP*TP*CP*CP*TP*AP*GP*AP*CP*TP*TP*GP*CP*CP*CP*A P*AP*TP*TP*A)-3') |   
F | DNA (5'-D(*AP*TP*AP*AP*TP*TP*GP*GP*GP*CP*AP*AP*GP*TP*CP*TP*A P*GP*GP*AP*A)-3') |   
  
Non-standard residues in 1tsr #2  
---  
ZN — zinc ion  
  

> select add #1

5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected  

> select add #2

11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected  

> hide sel atoms

> show sel cartoons

> select subtract #2

5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select add #2

5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected  

> select add #1

11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected  

> select subtract #2

5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select add #2

11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected  

> select subtract #2

5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected  

> select add #2

11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected  

> select subtract #1

5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected  

> select add #1

11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected  

> select subtract #1

5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected  

> select add #1

11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected  

> select subtract #1

5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected  

> select add #1

11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected  

> select subtract #1

5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected  

> select add #1

11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected  

> select subtract #1

5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected  

> select add #1

11656 atoms, 11298 bonds, 112 pseudobonds, 2028 residues, 6 models selected  

> select subtract #1

5828 atoms, 5649 bonds, 57 pseudobonds, 1014 residues, 3 models selected  

> close #2

> select add #1

5828 atoms, 5649 bonds, 55 pseudobonds, 1014 residues, 3 models selected  

> select subtract #1

Nothing selected  

> open 2ac0 fromDatabase pdb format mmcif

Summary of feedback from opening 2ac0 fetched from pdb  
---  
note | Fetching compressed mmCIF 2ac0 from http://files.rcsb.org/download/2ac0.cif  
  
2ac0 title:  
Structural Basis of DNA Recognition by p53 Tetramers (complex I) [more
info...]  
  
Chain information for 2ac0 #2  
---  
Chain | Description | UniProt  
A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-293  
E F G H | 5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3' |   
  
Non-standard residues in 2ac0 #2  
---  
ZN — zinc ion  
  
37 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!1 models

[deleted to fit within ticket limits]

> select add #2.4

8210 atoms, 272 bonds, 1896 residues, 8 models selected  

> select subtract #2.3

6658 atoms, 272 bonds, 1697 residues, 9 models selected  

> select subtract #2.8

6415 atoms, 272 bonds, 1685 residues, 8 models selected  

> select add #2.8

6658 atoms, 272 bonds, 1697 residues, 7 models selected  

> hide sel atoms

> select add #2.3

8210 atoms, 272 bonds, 1896 residues, 8 models selected  

> select subtract #2.4

6665 atoms, 272 bonds, 1698 residues, 9 models selected  

> select subtract #2.5

5136 atoms, 272 bonds, 1503 residues, 8 models selected  

> select subtract #2.6

3582 atoms, 272 bonds, 1305 residues, 7 models selected  

> select subtract #2.7

3339 atoms, 272 bonds, 1293 residues, 6 models selected  

> select subtract #2.8

3096 atoms, 272 bonds, 1281 residues, 5 models selected  

> select subtract #2.9

2853 atoms, 1269 residues, 4 models selected  

> select subtract #2.10

2610 atoms, 1257 residues, 3 models selected  

> show sel atoms

> select clear

> hide #!1 models

> select add #1.8

756 atoms, 648 bonds, 108 residues, 109 models selected  

> select subtract #1.8

Nothing selected  

> select add #1.7

435 atoms, 21 residues, 1 model selected  

> select subtract #1.7

1 model selected  

> show #!1 models

> hide #!1 models

> select add #2.9

243 atoms, 12 residues, 1 model selected  

> select add #2.10

486 atoms, 24 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> select add #2.8

729 atoms, 36 residues, 3 models selected  

> select add #2.7

972 atoms, 48 residues, 4 models selected  

> select subtract #2.9

729 atoms, 36 residues, 5 models selected  

> select subtract #2.10

486 atoms, 24 residues, 4 models selected  

> show sel atoms

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #2

8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 5 models selected  

> select subtract #2

8 models selected  

> hide #!2 models

> hide #!1 models

> show #!3 models

> select add #3.4

1558 atoms, 198 residues, 1 model selected  

> select add #3.5

3110 atoms, 395 residues, 2 models selected  

> select add #3.6

4662 atoms, 592 residues, 3 models selected  

> select add #3.7

5090 atoms, 613 residues, 4 models selected  

> select subtract #3.7

4662 atoms, 592 residues, 5 models selected  

> hide sel atoms

> show #!2 models

> hide #!2 models

> select add #3

7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 6 models selected  

> select subtract #3

6 models selected  

> show #!4 models

> hide #!3 models

> select add #4.10

243 atoms, 12 residues, 1 model selected  

> select subtract #4.10

1 model selected  

> select add #4.10

243 atoms, 12 residues, 1 model selected  

> select add #4.9

486 atoms, 24 residues, 2 models selected  

> select add #4.6

2010 atoms, 220 residues, 3 models selected  

> select add #4.5

3518 atoms, 413 residues, 4 models selected  

> select add #4.4

5056 atoms, 611 residues, 5 models selected  

> hide sel atoms

> show #!3 models

> hide #!3 models

> select add #4

8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 8 models selected  

> select subtract #4

8 models selected  

> show #!19 models

> select add #19.11

227 atoms, 12 residues, 1 model selected  

> select add #19.10

470 atoms, 24 residues, 2 models selected  

> select add #19.7

1954 atoms, 218 residues, 3 models selected  

> select add #19.6

3450 atoms, 411 residues, 4 models selected  

> select add #19.5

4939 atoms, 608 residues, 5 models selected  

> hide sel atoms

> select add #19

7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 9 models selected  

> select subtract #19

8 models selected  

Cell requested for row 17 is out of bounds for table with 30 rows! Resizing
table model.  

> show #!18 models

> hide #!19 models

> select add #18.6

1848 atoms, 231 residues, 1 model selected  

> select add #18.5

3696 atoms, 462 residues, 2 models selected  

> select add #18.4

5544 atoms, 693 residues, 3 models selected  

> hide sel atoms

> select add #18.7

6071 atoms, 719 residues, 4 models selected  

> select subtract #18.7

5544 atoms, 693 residues, 5 models selected  

> hide #!18 models

> show #!17 models

> select add #18

8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 6 models selected  

> select subtract #18

6 models selected  

> select add #17.6

1863 atoms, 234 residues, 1 model selected  

> select add #17.5

3726 atoms, 468 residues, 2 models selected  

> select add #17.4

5589 atoms, 702 residues, 3 models selected  

> hide sel atoms

> select add #17

8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 6 models selected  

> select subtract #17

6 models selected  

Cell requested for row 15 is out of bounds for table with 27 rows! Resizing
table model.  

> show #!16 models

> hide #!17 models

> select add #16.5

410 atoms, 20 residues, 1 model selected  

> select subtract #16.5

1 model selected  

> select add #16.4

1486 atoms, 195 residues, 1 model selected  

> hide sel atoms

> select add #16.1

1486 atoms, 8 pseudobonds, 195 residues, 3 models selected  

> select subtract #16.1

1486 atoms, 195 residues, 2 models selected  

> select add #16.2

1486 atoms, 2 pseudobonds, 195 residues, 3 models selected  

> select subtract #16.2

1486 atoms, 195 residues, 2 models selected  

> select add #16.3

2972 atoms, 390 residues, 2 models selected  

> select subtract #16.3

1486 atoms, 195 residues, 3 models selected  

> select add #16

3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 4 models selected  

> select subtract #16

3 models selected  

> hide #!16 models

> show #!16 models

> show #!15 models

> hide #!16 models

> show #!14 models

> show #!13 models

> hide #!14 models

> hide #!15 models

> hide #15.1 models

> show #15.1 models

> hide #!15 models

> select add #13.8

388 atoms, 19 residues, 1 model selected  

> select subtract #13.8

1 model selected  

> select add #13.6

1571 atoms, 200 residues, 1 model selected  

> select add #13.5

3142 atoms, 400 residues, 2 models selected  

> select add #13.4

4713 atoms, 600 residues, 3 models selected  

> hide sel atoms

> select add #13

7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 6 models selected  

> select subtract #13

6 models selected  

> show #!12 models

> hide #!13 models

> select add #12.8

526 atoms, 26 residues, 1 model selected  

> select subtract #12.8

1 model selected  

> select add #12.6

1863 atoms, 234 residues, 1 model selected  

> select add #12.5

3726 atoms, 468 residues, 2 models selected  

> select add #12.4

5589 atoms, 702 residues, 3 models selected  

> hide sel atoms

> select add #12

8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 6 models selected  

> select subtract #12

6 models selected  

> show #!11 models

> hide #!12 models

> select add #11.6

1571 atoms, 200 residues, 1 model selected  

> select add #11.5

3142 atoms, 400 residues, 2 models selected  

> select add #11.4

4713 atoms, 600 residues, 3 models selected  

> hide sel atoms

> select add #11.7

5141 atoms, 621 residues, 4 models selected  

> select subtract #11.7

4713 atoms, 600 residues, 5 models selected  

> select subtract #11.6

3142 atoms, 400 residues, 4 models selected  

> select subtract #11.5

1571 atoms, 200 residues, 3 models selected  

> select subtract #11.4

1 model selected  

> show #!10 models

> hide #!11 models

> hide #!10 models

> show #!10 models

> hide #!4 models

> show #!9 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!8 models

> hide #!9 models

> select add #8.10

243 atoms, 12 residues, 1 model selected  

> select add #8.9

486 atoms, 24 residues, 2 models selected  

> select add #8.6

2005 atoms, 220 residues, 3 models selected  

> select add #8.5

3519 atoms, 415 residues, 4 models selected  

> select add #8.4

5060 atoms, 613 residues, 5 models selected  

> hide sel atoms

> select add #8

8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 8 models selected  

> select subtract #8

8 models selected  

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!7 models

> select add #7.6

1865 atoms, 234 residues, 1 model selected  

> select add #7.5

3730 atoms, 468 residues, 2 models selected  

> select add #7.4

5595 atoms, 702 residues, 3 models selected  

> hide sel atoms

> select add #7

8593 atoms, 8812 bonds, 73 pseudobonds, 1061 residues, 6 models selected  

> select subtract #7

6 models selected  

> show #!6 models

> hide #!7 models

> hide #!6 models

> show #!6 models

> show #!5 models

> hide #!6 models

> select add #5.9

243 atoms, 12 residues, 1 model selected  

> select add #5.10

466 atoms, 23 residues, 2 models selected  

> select add #5.6

2002 atoms, 221 residues, 3 models selected  

> select add #5.5

3537 atoms, 417 residues, 4 models selected  

> select add #5.4

5089 atoms, 616 residues, 5 models selected  

> hide sel atoms

> select add #5

7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 8 models selected  

> select subtract #5

8 models selected  

> show #!4 models

> hide #!5 models

> show #!3 models

> hide #!4 models

> show #!1 models

> show #!2 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!19 models

> show #!18 models

> show #!17 models

> show #!16 models

Drag select of 883 atoms, 15 bonds  

> hide sel atoms

Drag select of 560 atoms, 6 bonds  

> hide sel atoms

Drag select of 49 atoms  

> hide sel atoms

Drag select of 358 atoms, 3 bonds  

> hide sel atoms

Drag select of 604 atoms  

> hide sel atoms

Drag select of 106 atoms  

> hide sel atoms

Drag select of 22 atoms  

> hide sel atoms

Drag select of 610 atoms, 3 bonds  

> hide sel atoms

Drag select of 112 atoms  

> hide sel atoms

Drag select of 252 atoms, 1 bonds  

> hide sel atoms

Drag select of 4 atoms  

> hide sel atoms

Drag select of 3 atoms  

> hide sel atoms

Drag select of 47 atoms, 8 bonds  

> hide sel atoms

Drag select of 77 atoms  

> hide sel atoms

Drag select of 15 atoms  

> hide sel atoms

> select ions

61 atoms, 61 residues, 19 models selected  

> select solvent

8211 atoms, 8211 residues, 18 models selected  

> hide sel atoms

> save "/Users/kompa012/Desktop/P53/Before mutation 1.cxs"

> hide #!2 models

> show #!2 models

> hide #!2 models

> select #!1/B:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #!1/B:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 12 atom styles  

> style sel stick

Changed 12 atom styles  

> show #!2 models

> select Y220

Expected an objects specifier or a keyword  

> select #1 Y220

Expected a keyword  

> select #1, Y220

Expected an objects specifier or a keyword  

> select #1 :Y220

Nothing selected  

> select #1-19 :Y220

Nothing selected  

> select #1-19 :220

698 atoms, 696 bonds, 60 residues, 19 models selected  

> select #1-19 /A :220

228 atoms, 228 bonds, 19 residues, 19 models selected  

> style sel sphere

Changed 228 atom styles  

> style sel stick

Changed 228 atom styles  

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> hide #!10 models

> show #!9 models

> show #!10 models

> select add #9.2

228 atoms, 228 bonds, 1 pseudobond, 19 residues, 37 models selected  

> select subtract #9.2

228 atoms, 228 bonds, 19 residues, 36 models selected  

> select add #9.1

228 atoms, 228 bonds, 4 pseudobonds, 19 residues, 37 models selected  

> select subtract #9.1

228 atoms, 228 bonds, 19 residues, 36 models selected  

> select clear

> select ligand

172 atoms, 129 bonds, 43 residues, 4 models selected  

> hide sel atoms

> select add #8

8188 atoms, 7432 bonds, 81 pseudobonds, 1838 residues, 6 models selected  

> select subtract #8

100 atoms, 75 bonds, 25 residues, 11 models selected  

> select add #9

2021 atoms, 1891 bonds, 5 pseudobonds, 398 residues, 5 models selected  

> select subtract #9

72 atoms, 54 bonds, 18 residues, 2 models selected  

> select add #10

2176 atoms, 1883 bonds, 5 pseudobonds, 563 residues, 4 models selected  

> select subtract #10

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1-19 /A :220

228 atoms, 228 bonds, 19 residues, 19 models selected  

> select subtract #1.3

216 atoms, 216 bonds, 18 residues, 35 models selected  

> lighting full

> lighting simple

> lighting soft

Cell requested for row 8 is out of bounds for table with 28 rows! Resizing
table model.  

> select add #1.9

228 atoms, 225 bonds, 21 residues, 38 models selected  

> select add #1.8

984 atoms, 873 bonds, 129 residues, 147 models selected  

> select clear

> select add #1.8

756 atoms, 648 bonds, 108 residues, 109 models selected  

> select add #1.9

768 atoms, 657 bonds, 111 residues, 113 models selected  

> hide sel atoms

> select add #1

6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected  

> select subtract #1

5 models selected  

> select #1-19 /A :220

228 atoms, 228 bonds, 19 residues, 19 models selected  

> color (#!1-19 & sel) black

> style sel sphere

Changed 228 atom styles  

> select #1-19 /A :248

207 atoms, 188 bonds, 19 residues, 19 models selected  

> select add #1

6792 atoms, 6484 bonds, 55 pseudobonds, 1143 residues, 151 models selected  

> select subtract #1

196 atoms, 178 bonds, 18 residues, 39 models selected  

> color (#!2-19 & sel) black

> style sel sphere

Changed 196 atom styles  

> select #1-19 /A :282

209 atoms, 190 bonds, 19 residues, 19 models selected  

> color (#!1-19 & sel) black

> style sel sphere

Changed 209 atom styles  

> ui tool show "Color Actions"

> select clear

> set bgColor white

> set bgColor #ffffff00

> lighting flat

> select #1-19 /A :282

209 atoms, 190 bonds, 19 residues, 19 models selected  

> lighting full

> graphics silhouettes false

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> select clear

> color #1 #0009d1ff

> color #1 #0017d1ff

> color #1 #00d1c3ff

> color #1 #00d1b9ff

> color #1 #74d100ff

> color #1 #70d100ff

> color #1 #5bd100ff

> color #1 #60d100ff

> color #2 #85d406ff

> color #2 #87d401ff

> color #3 #b1dc05ff

> color #4 #d0d405ff

> color #5 #d4ba04ff

> color #6 #db9704ff

> color #7 #d16404ff

> color #8 #f4520cff

> color #9 #ff2f10ff

> color #10 #940907ff

> color #9 #ff1f1aff

> color #10 #a71728ff

> color #11 #fc1a3dff

> color #10 #ff3b4cff

> color #10 #ff1ed9ff

> color #10 #ff08ceff

> color #10 #ff00efff

> color #9 #ff00adff

> color #11 #e406ffff

> color #12 #ce02fcff

> color #13 #b700fcff

> color #14 #826cffff

> color #14 #b000ffff

> color #14 #ad00ffff

> color #15 #ff7c70ff

> color #15 #8308ffff

> color #16 #edff78ff

> color #16 #3907ffff

> color #16 #4a11ffff

> color #17 #0d00fcff

> color #18 #0040e1ff

> color #19 #008afaff

> select #1-19 /A :282

209 atoms, 190 bonds, 19 residues, 19 models selected  

> color (#!1-19 & sel) black

> select #1-19 /A :248

207 atoms, 188 bonds, 19 residues, 19 models selected  

> color (#!1-19 & sel) black

> select #1-19 /A :220

228 atoms, 228 bonds, 19 residues, 19 models selected  

> color (#!1-19 & sel) black

> select clear

> select #!1/B:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #!1/B:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 12 atom styles  

> color (#!1 & sel) black

> select #!1/B:282

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #!1/B:282

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 11 atom styles  

> color (#!1 & sel) black

> select #!1/B:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #!1/B:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #!1/B:248

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #!1/B:248

11 atoms, 10 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 11 atom styles  

> color (#!1 & sel) black

> select clear

> lighting flat

> lighting simple

> lighting shadows true

> lighting shadows false

> ui tool show "Side View"

> select add #8

8088 atoms, 7357 bonds, 81 pseudobonds, 1813 residues, 3 models selected  

> select add #9

10037 atoms, 9194 bonds, 86 pseudobonds, 2193 residues, 14 models selected  

> select add #10

12209 atoms, 11074 bonds, 91 pseudobonds, 2755 residues, 17 models selected  

> select add #11

20184 atoms, 18460 bonds, 154 pseudobonds, 4433 residues, 20 models selected  

> select add #12

28805 atoms, 27260 bonds, 225 pseudobonds, 5530 residues, 29 models selected  

> select add #13

36392 atoms, 34558 bonds, 289 pseudobonds, 6895 residues, 38 models selected  

> select add #14

38485 atoms, 36372 bonds, 294 pseudobonds, 7442 residues, 47 models selected  

> select add #15

40594 atoms, 38199 bonds, 299 pseudobonds, 7993 residues, 52 models selected  

> select add #16

44291 atoms, 41698 bonds, 309 pseudobonds, 8718 residues, 57 models selected  

> select add #17

52968 atoms, 50498 bonds, 386 pseudobonds, 9871 residues, 63 models selected  

> select add #18

61424 atoms, 59238 bonds, 445 pseudobonds, 10851 residues, 72 models selected  

> select add #19

69057 atoms, 66350 bonds, 526 pseudobonds, 12429 residues, 82 models selected  

> select add #7

77650 atoms, 75162 bonds, 599 pseudobonds, 13490 residues, 93 models selected  

> select add #6

79582 atoms, 76997 bonds, 603 pseudobonds, 13856 residues, 101 models selected  

> select add #5

87363 atoms, 84304 bonds, 673 pseudobonds, 15411 residues, 106 models selected  

> select add #4

95398 atoms, 91585 bonds, 747 pseudobonds, 17244 residues, 117 models selected  

> select add #3

102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 128 models
selected  

> select add #2

110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 137 models
selected  

> select add #1

117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 261 models
selected  

> color (#1.8.1-108#1.9.1-3#!1-19 & sel) dark gray

> select #1-19 /A :220

228 atoms, 228 bonds, 19 residues, 19 models selected  

> color (#!1-19 & sel) black

> select #1-19 /A :248

207 atoms, 188 bonds, 19 residues, 19 models selected  

> color (#!1-19 & sel) black

> select #1-19 /A :282

209 atoms, 190 bonds, 19 residues, 19 models selected  

> color (#!1-19 & sel) black

> select #!1/B:248

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #!1/B:248

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) black

> select #!1/B:167-170,177-181,278-287

167 atoms, 169 bonds, 19 residues, 1 model selected  

> select #!1/B:282

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #!1/B:282

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) black

> select #!1/B:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #!1/B:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) black

> select clear

Cell requested for row 15 is out of bounds for table with 28 rows! Resizing
table model.  

> select #1-19 :AP, TP, GP, CP

Nothing selected  

> select #1-19 :AP

Nothing selected  

> select add #3

7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 3 models selected  

> select add #4

15128 atoms, 14594 bonds, 131 pseudobonds, 2688 residues, 12 models selected  

> select add #5

22909 atoms, 21901 bonds, 201 pseudobonds, 4243 residues, 23 models selected  

> select add #6

24841 atoms, 23736 bonds, 205 pseudobonds, 4609 residues, 33 models selected  

> select add #7

33434 atoms, 32548 bonds, 278 pseudobonds, 5670 residues, 38 models selected  

> select add #8

41522 atoms, 39905 bonds, 359 pseudobonds, 7483 residues, 47 models selected  

> select add #9

43471 atoms, 41742 bonds, 364 pseudobonds, 7863 residues, 58 models selected  

> select add #10

45643 atoms, 43622 bonds, 369 pseudobonds, 8425 residues, 61 models selected  

> select add #11

53618 atoms, 51008 bonds, 432 pseudobonds, 10103 residues, 64 models selected  

> select add #12

62239 atoms, 59808 bonds, 503 pseudobonds, 11200 residues, 73 models selected  

> select add #13

69826 atoms, 67106 bonds, 567 pseudobonds, 12565 residues, 82 models selected  

> select add #14

71919 atoms, 68920 bonds, 572 pseudobonds, 13112 residues, 91 models selected  

> select add #15

74028 atoms, 70747 bonds, 577 pseudobonds, 13663 residues, 96 models selected  

> select add #16

77725 atoms, 74246 bonds, 587 pseudobonds, 14388 residues, 101 models selected  

> select add #17

86402 atoms, 83046 bonds, 664 pseudobonds, 15541 residues, 107 models selected  

> select add #18

94858 atoms, 91786 bonds, 723 pseudobonds, 16521 residues, 116 models selected  

> select add #19

102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 126 models
selected  

> show sel cartoons

> select add #1

109087 atoms, 105204 bonds, 859 pseudobonds, 19224 residues, 250 models
selected  

> select add #2

117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 258 models
selected  

> select subtract #19.4

115783 atoms, 111064 bonds, 933 pseudobonds, 20924 residues, 266 models
selected  

> select subtract #19.11

115556 atoms, 110812 bonds, 898 pseudobonds, 20912 residues, 265 models
selected  

> select subtract #19.10

115313 atoms, 110540 bonds, 898 pseudobonds, 20900 residues, 264 models
selected  

> hide #!18 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> select subtract #1

108717 atoms, 104234 bonds, 843 pseudobonds, 19775 residues, 147 models
selected  

> select subtract #2

100507 atoms, 96826 bonds, 765 pseudobonds, 17879 residues, 139 models
selected  

> select subtract #3

93414 atoms, 89513 bonds, 708 pseudobonds, 17024 residues, 128 models selected  

> select subtract #4

85379 atoms, 82232 bonds, 634 pseudobonds, 15191 residues, 119 models selected  

> select subtract #5

77598 atoms, 74925 bonds, 564 pseudobonds, 13636 residues, 108 models selected  

> select subtract #6

75666 atoms, 73090 bonds, 560 pseudobonds, 13270 residues, 98 models selected  

> select subtract #7

67073 atoms, 64278 bonds, 487 pseudobonds, 12209 residues, 93 models selected  

> select subtract #9

65124 atoms, 62441 bonds, 482 pseudobonds, 11829 residues, 84 models selected  

> select subtract #8

57036 atoms, 55084 bonds, 401 pseudobonds, 10016 residues, 81 models selected  

> select subtract #10

54864 atoms, 53204 bonds, 396 pseudobonds, 9454 residues, 70 models selected  

> select subtract #11

46889 atoms, 45818 bonds, 333 pseudobonds, 7776 residues, 67 models selected  

> select subtract #12

38268 atoms, 37018 bonds, 262 pseudobonds, 6679 residues, 58 models selected  

> select subtract #13

30681 atoms, 29720 bonds, 198 pseudobonds, 5314 residues, 49 models selected  

> select subtract #14

28588 atoms, 27906 bonds, 193 pseudobonds, 4767 residues, 40 models selected  

> select subtract #15

26479 atoms, 26079 bonds, 188 pseudobonds, 4216 residues, 35 models selected  

> select subtract #16

22782 atoms, 22580 bonds, 178 pseudobonds, 3491 residues, 30 models selected  

> select subtract #17

14105 atoms, 13780 bonds, 101 pseudobonds, 2338 residues, 24 models selected  

> select subtract #18

5649 atoms, 5040 bonds, 42 pseudobonds, 1358 residues, 15 models selected  

> select add #19.10

5892 atoms, 5040 bonds, 42 pseudobonds, 1370 residues, 9 models selected  

> select add #19.11

6119 atoms, 5040 bonds, 42 pseudobonds, 1382 residues, 10 models selected  

> select subtract #19.9

5903 atoms, 4802 bonds, 12 pseudobonds, 1371 residues, 9 models selected  

> select subtract #19.8

5690 atoms, 4566 bonds, 12 pseudobonds, 1359 residues, 8 models selected  

> hide sel atoms

> hide sel cartoons

> select add #8

13778 atoms, 11923 bonds, 93 pseudobonds, 3172 residues, 10 models selected  

> select subtract #8

5690 atoms, 4566 bonds, 12 pseudobonds, 1359 residues, 15 models selected  

> select add #19

7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 9 models selected  

> select subtract #19

8 models selected  

> hide #!19 models

> show #!19 models

> show #!18 models

> show #!17 models

> show #!16 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #!12 models

> show #!11 models

> show #!10 models

> show #!9 models

> show #!8 models

> show #!7 models

> show #!6 models

> show #!5 models

> show #!4 models

> show #!3 models

> show #!2 models

> show #!1 models

> select add #1

6596 atoms, 6306 bonds, 55 pseudobonds, 1125 residues, 116 models selected  

> select add #2

14806 atoms, 13714 bonds, 133 pseudobonds, 3021 residues, 124 models selected  

> select add #3

21899 atoms, 21027 bonds, 190 pseudobonds, 3876 residues, 135 models selected  

> select add #4

29934 atoms, 28308 bonds, 264 pseudobonds, 5709 residues, 144 models selected  

> select add #5

37715 atoms, 35615 bonds, 334 pseudobonds, 7264 residues, 155 models selected  

> select add #6

39647 atoms, 37450 bonds, 338 pseudobonds, 7630 residues, 165 models selected  

> select add #7

48240 atoms, 46262 bonds, 411 pseudobonds, 8691 residues, 170 models selected  

> select add #9

50189 atoms, 48099 bonds, 416 pseudobonds, 9071 residues, 179 models selected  

> select add #8

58277 atoms, 55456 bonds, 497 pseudobonds, 10884 residues, 182 models selected  

> select add #10

60449 atoms, 57336 bonds, 502 pseudobonds, 11446 residues, 193 models selected  

> select add #11

68424 atoms, 64722 bonds, 565 pseudobonds, 13124 residues, 196 models selected  

> select add #12

77045 atoms, 73522 bonds, 636 pseudobonds, 14221 residues, 205 models selected  

> select add #13

84632 atoms, 80820 bonds, 700 pseudobonds, 15586 residues, 214 models selected  

> select add #14

86725 atoms, 82634 bonds, 705 pseudobonds, 16133 residues, 223 models selected  

> select add #15

88834 atoms, 84461 bonds, 710 pseudobonds, 16684 residues, 228 models selected  

> select add #16

92531 atoms, 87960 bonds, 720 pseudobonds, 17409 residues, 233 models selected  

> select add #17

101208 atoms, 96760 bonds, 797 pseudobonds, 18562 residues, 239 models
selected  

> select add #18

109664 atoms, 105500 bonds, 856 pseudobonds, 19542 residues, 248 models
selected  

> select add #19

117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 258 models
selected  

> hide sel cartoons

> nucleotides sel atoms

> style nucleic & sel stick

Changed 13700 atom styles  

> nucleotides sel tube/slab shape box

> select subtract #1

110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 150 models
selected  

> select add #1.7

111136 atoms, 106306 bonds, 882 pseudobonds, 20016 residues, 146 models
selected  

> select subtract #1.7

110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 146 models
selected  

> select add #1.7

111136 atoms, 106306 bonds, 882 pseudobonds, 20016 residues, 146 models
selected  

> select add #1.6

111556 atoms, 106306 bonds, 882 pseudobonds, 20037 residues, 147 models
selected  

> select add #1

117297 atoms, 112612 bonds, 937 pseudobonds, 21120 residues, 263 models
selected  

> select subtract #1

110701 atoms, 106306 bonds, 882 pseudobonds, 19995 residues, 150 models
selected  

> select subtract #2

102491 atoms, 98898 bonds, 804 pseudobonds, 18099 residues, 142 models
selected  

> select subtract #3

95398 atoms, 91585 bonds, 747 pseudobonds, 17244 residues, 131 models selected  

> select subtract #4

87363 atoms, 84304 bonds, 673 pseudobonds, 15411 residues, 122 models selected  

> select subtract #5

79582 atoms, 76997 bonds, 603 pseudobonds, 13856 residues, 111 models selected  

> select subtract #6

77650 atoms, 75162 bonds, 599 pseudobonds, 13490 residues, 101 models selected  

> select subtract #7

69057 atoms, 66350 bonds, 526 pseudobonds, 12429 residues, 96 models selected  

> select subtract #8

60969 atoms, 58993 bonds, 445 pseudobonds, 10616 residues, 87 models selected  

> select subtract #9

59020 atoms, 57156 bonds, 440 pseudobonds, 10236 residues, 76 models selected  

> select subtract #10

56848 atoms, 55276 bonds, 435 pseudobonds, 9674 residues, 73 models selected  

> select subtract #12

48227 atoms, 46476 bonds, 364 pseudobonds, 8577 residues, 70 models selected  

> select subtract #13

40640 atoms, 39178 bonds, 300 pseudobonds, 7212 residues, 61 models selected  

> select subtract #11

32665 atoms, 31792 bonds, 237 pseudobonds, 5534 residues, 52 models selected  

> select subtract #14

30572 atoms, 29978 bonds, 232 pseudobonds, 4987 residues, 43 models selected  

> select subtract #15

28463 atoms, 28151 bonds, 227 pseudobonds, 4436 residues, 38 models selected  

> select subtract #16

24766 atoms, 24652 bonds, 217 pseudobonds, 3711 residues, 33 models selected  

> select subtract #17

16089 atoms, 15852 bonds, 140 pseudobonds, 2558 residues, 27 models selected  

> select subtract #18

7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 18 models selected  

> select subtract #19

8 models selected  

> select add #1.7

435 atoms, 21 residues, 1 model selected  

> select add #1.6

855 atoms, 42 residues, 2 models selected  

> show sel cartoons

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!12 models

> hide #!11 models

> show #!11 models

> hide #!10 models

> hide #!11 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> color (#!1 & sel) blue

> select subtract #1.6

435 atoms, 21 residues, 3 models selected  

> select subtract #1.7

1 model selected  

> select add #1.4

1522 atoms, 194 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select #1-19 /A :282

209 atoms, 190 bonds, 19 residues, 19 models selected  

> show sel & #!1 atoms

> select subtract #1.3

198 atoms, 180 bonds, 18 residues, 35 models selected  

> select add #1.3

1733 atoms, 180 bonds, 214 residues, 35 models selected  

> hide sel & #!1 atoms

> select clear

> show #!2 models

> select add #2

8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 3 models selected  

> hide sel atoms

> select subtract #2

8 models selected  

> select add #2.10

243 atoms, 12 residues, 1 model selected  

> select subtract #2.10

1 model selected  

> select add #2.10

243 atoms, 12 residues, 1 model selected  

> select add #2.9

486 atoms, 24 residues, 2 models selected  

> select subtract #2.10

243 atoms, 12 residues, 3 models selected  

> select subtract #2.9

1 model selected  

> select add #2.8

243 atoms, 12 residues, 1 model selected  

> select add #2.7

486 atoms, 24 residues, 2 models selected  

> show sel cartoons

> select subtract #2.7

243 atoms, 12 residues, 3 models selected  

> select subtract #2.8

1 model selected  

> select add #2.3

1552 atoms, 199 residues, 1 model selected  

> show sel cartoons

> select add #2.8

1795 atoms, 211 residues, 2 models selected  

> select add #2.7

2038 atoms, 223 residues, 3 models selected  

> select subtract #2.3

486 atoms, 24 residues, 4 models selected  

> color (#!2 & sel) blue

> select add #2

8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 5 models selected  

> select subtract #2

8 models selected  

> show #!3 models

> select add #3.8

427 atoms, 21 residues, 1 model selected  

> select add #3.7

855 atoms, 42 residues, 2 models selected  

> show sel cartoons

> color (#!3 & sel) blue

> select subtract #3.7

427 atoms, 21 residues, 3 models selected  

> select subtract #3.8

1 model selected  

> select add #3.3

1552 atoms, 197 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

Cell requested for row 8 is out of bounds for table with 27 rows! Resizing
table model.  

> select add #3

7093 atoms, 7313 bonds, 57 pseudobonds, 855 residues, 4 models selected  

> select subtract #3

6 models selected  

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> show #!4 models

> select add #4.10

243 atoms, 12 residues, 1 model selected  

> select subtract #4.10

1 model selected  

> select add #4.8

224 atoms, 11 residues, 1 model selected  

> select add #4.7

426 atoms, 21 residues, 2 models selected  

> select add #4.3

1977 atoms, 220 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> show sel atoms

> select subtract #4.7

1775 atoms, 210 residues, 4 models selected  

> select subtract #4.8

1551 atoms, 199 residues, 3 models selected  

> hide sel atoms

> select subtract #4.3

1 model selected  

> select add #4.8

224 atoms, 11 residues, 1 model selected  

> select add #4.7

426 atoms, 21 residues, 2 models selected  

> color (#!4 & sel) blue

> show #!5 models

> select add #4

8035 atoms, 7281 bonds, 74 pseudobonds, 1833 residues, 5 models selected  

> select subtract #4

8 models selected  

> select add #5.8

222 atoms, 11 residues, 1 model selected  

> select add #5.7

425 atoms, 21 residues, 2 models selected  

> show sel cartoons

> color (#!5 & sel) blue

> select subtract #5.8

203 atoms, 10 residues, 3 models selected  

> select subtract #5.7

1 model selected  

> select add #5.3

1546 atoms, 197 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select add #5

7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 4 models selected  

> select subtract #5

8 models selected  

> show #!6 models

> select add #6

1932 atoms, 1835 bonds, 4 pseudobonds, 366 residues, 2 models selected  

> select subtract #6

2 models selected  

> select add #6.3

205 atoms, 10 residues, 1 model selected  

> show sel cartoons

> color (#!6 & sel) blue

> select subtract #6.3

1 model selected  

> select add #6.2

1571 atoms, 200 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select add #6

1932 atoms, 1835 bonds, 4 pseudobonds, 366 residues, 3 models selected  

> select subtract #6

2 models selected  

> hide #!6 models

> select add #5

7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 3 models selected  

> select subtract #5

8 models selected  

> select add #5.3

1546 atoms, 197 residues, 1 model selected  

> show sel cartoons

> select add #5

7781 atoms, 7307 bonds, 70 pseudobonds, 1555 residues, 4 models selected  

> select subtract #5

8 models selected  

> show #!6 models

> show #!7 models

> select add #7.8

535 atoms, 26 residues, 1 model selected  

> select add #7.7

1060 atoms, 52 residues, 2 models selected  

> show sel cartoons

> color (#!7 & sel) blue

> select subtract #7.7

535 atoms, 26 residues, 3 models selected  

> select subtract #7.8

1 model selected  

> select add #7.3

1865 atoms, 234 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select subtract #7.3

1 model selected  

> show #!8 models

> select add #8.8

227 atoms, 11 residues, 1 model selected  

> select add #8.7

448 atoms, 22 residues, 2 models selected  

> show sel cartoons

> color (#!8 & sel) blue

> select subtract #8.7

227 atoms, 11 residues, 3 models selected  

> select subtract #8.8

1 model selected  

> select add #8.3

1545 atoms, 197 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel cartoons

> select subtract #8.3

1 model selected  

> show #!9 models

> select add #9.2

1 pseudobond, 1 model selected  

> select subtract #9.2

Nothing selected  

> select add #9

1949 atoms, 1837 bonds, 5 pseudobonds, 380 residues, 3 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #9

2 models selected  

> select add #9.4

221 atoms, 11 residues, 1 model selected  

> nucleotides sel tube/slab shape box

> show sel cartoons

> color (#!9 & sel) blue

> select subtract #9.4

1 model selected  

> select add #9.3

1535 atoms, 197 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select add #9

1949 atoms, 1837 bonds, 5 pseudobonds, 380 residues, 4 models selected  

> select subtract #9

2 models selected  

> show #!10 models

> select add #10

2172 atoms, 1880 bonds, 5 pseudobonds, 562 residues, 3 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #10.4

1947 atoms, 1629 bonds, 5 pseudobonds, 550 residues, 5 models selected  

> select subtract #10.3

404 atoms, 51 bonds, 353 residues, 2 models selected  

> select add #10.3

1947 atoms, 51 bonds, 550 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select add #10.4

2172 atoms, 51 bonds, 562 residues, 2 models selected  

> select subtract #10.3

629 atoms, 51 bonds, 365 residues, 3 models selected  

> show sel cartoons

> color (#!10 & sel) blue

> select add #10

2172 atoms, 1880 bonds, 5 pseudobonds, 562 residues, 4 models selected  

> select subtract #10

2 models selected  

> show #!11 models

> hide #!10 models

> hide #!11 models

> show #!10 models

> show #!11 models

> select add #11.3

1571 atoms, 200 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select add #11.7

1999 atoms, 221 residues, 2 models selected  

> select add #11.8

2426 atoms, 242 residues, 3 models selected  

> select subtract #11.3

855 atoms, 42 residues, 4 models selected  

> show sel cartoons

> color (#!11 & sel) blue

> select add #11

7975 atoms, 7386 bonds, 63 pseudobonds, 1678 residues, 5 models selected  

> select subtract #11

6 models selected  

> show #!12 models

> select add #12.8

526 atoms, 26 residues, 1 model selected  

> select add #12.7

1060 atoms, 52 residues, 2 models selected  

> show sel cartoons

> color (#!12 & sel) blue

> select subtract #12.7

526 atoms, 26 residues, 3 models selected  

> select subtract #12.8

1 model selected  

> select add #12.4

1863 atoms, 234 residues, 1 model selected  

> select subtract #12.4

1 model selected  

> select add #12.3

1863 atoms, 234 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> show #!13 models

> select add #12

8621 atoms, 8800 bonds, 71 pseudobonds, 1097 residues, 4 models selected  

> select subtract #12

6 models selected  

> select add #13.3

1571 atoms, 200 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select subtract #13.3

1 model selected  

> select add #13.8

388 atoms, 19 residues, 1 model selected  

> select add #13.7

776 atoms, 38 residues, 2 models selected  

> show sel cartoons

> color (#!13 & sel) blue

> select add #13

7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 5 models selected  

> select subtract #13

6 models selected  

> show #!14 models

> select add #14.4

225 atoms, 12 residues, 1 model selected  

> show sel cartoons

> color (#!14 & sel) blue

> select add #14.3

1755 atoms, 209 residues, 2 models selected  

> select subtract #14.4

1530 atoms, 197 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> select add #14

2093 atoms, 1814 bonds, 5 pseudobonds, 547 residues, 4 models selected  

> select subtract #14

2 models selected  

> show #!15 models

> select add #15.4

225 atoms, 12 residues, 1 model selected  

> show sel cartoons

> color (#!15 & sel) blue

> select add #15.3

1764 atoms, 209 residues, 2 models selected  

> select subtract #15.4

1539 atoms, 197 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select add #15

2109 atoms, 1827 bonds, 5 pseudobonds, 551 residues, 4 models selected  

> select subtract #15

2 models selected  

> show #!16 models

> select add #16.5

410 atoms, 20 residues, 1 model selected  

> color (#!16 & sel) blue

> show sel cartoons

> select add #16.4

1896 atoms, 215 residues, 2 models selected  

> select subtract #16.5

1486 atoms, 195 residues, 3 models selected  

> select add #16.5

1896 atoms, 215 residues, 2 models selected  

> select subtract #16.5

1486 atoms, 195 residues, 3 models selected  

> select add #16.3

2972 atoms, 390 residues, 2 models selected  

> select subtract #16.4

1486 atoms, 195 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> select add #16.4

2972 atoms, 390 residues, 2 models selected  

> select subtract #16.4

1486 atoms, 195 residues, 3 models selected  

> select subtract #16.3

1 model selected  

> show #!17 models

> select add #17.8

533 atoms, 26 residues, 1 model selected  

> select add #17.7

1060 atoms, 52 residues, 2 models selected  

> show sel cartoons

> color (#!17 & sel) blue

> select subtract #17.7

533 atoms, 26 residues, 3 models selected  

> select subtract #17.8

1 model selected  

> select add #17.3

1863 atoms, 234 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select add #17

8677 atoms, 8800 bonds, 77 pseudobonds, 1153 residues, 4 models selected  

> select subtract #17

6 models selected  

> show #!18 models

> select add #18.8

533 atoms, 26 residues, 1 model selected  

> select add #18.7

1060 atoms, 52 residues, 2 models selected  

> color (#!18 & sel) blue

> show sel cartoons

> select subtract #18.7

533 atoms, 26 residues, 3 models selected  

> select subtract #18.8

1 model selected  

> select add #18.3

1848 atoms, 231 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select add #18

8456 atoms, 8740 bonds, 59 pseudobonds, 980 residues, 4 models selected  

> select subtract #18

6 models selected  

> show #!19 models

> select add #19.11

227 atoms, 12 residues, 1 model selected  

> select subtract #19.11

1 model selected  

> select add #19.9

216 atoms, 11 residues, 1 model selected  

> select add #19.8

429 atoms, 23 residues, 2 models selected  

> show sel cartoons

> color (#!19 & sel) blue

> select subtract #19.8

216 atoms, 11 residues, 3 models selected  

> select subtract #19.9

1 model selected  

> select add #19.4

1514 atoms, 196 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select add #19

7633 atoms, 7112 bonds, 81 pseudobonds, 1578 residues, 5 models selected  

> select subtract #19

8 models selected  

> select #1-19 /A :282

209 atoms, 190 bonds, 19 residues, 19 models selected  

> show sel atoms

> select #1-19 /A :248

207 atoms, 188 bonds, 19 residues, 19 models selected  

> show sel atoms

> select #1-19 /A :220

228 atoms, 228 bonds, 19 residues, 19 models selected  

> show sel atoms

Drag select of 23 atoms  

> hide sel atoms

Drag select of 11 atoms, 10 bonds  

> hide sel atoms

> select #!1/B:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #!1/B:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #!1/B:248

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #!1/B:248

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #!1/B:282

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #!1/B:282

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

Drag select of 123 residues, 341 shapes, 1 atoms  

> hide sel cartoons

> hide sel atoms

> select clear

> save "/Users/kompa012/Desktop/P53/Superposition of P53.png" width 3000
> height 2520 supersample 3 transparentBackground true

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> hide #!18 models

> hide #!19 models

> save /Users/kompa012/Desktop/P53/1tup.png width 3000 height 2520 supersample
> 3 transparentBackground true

> show #!2 models

> hide #!1 models

> select add #2.8

243 atoms, 12 residues, 1 model selected  

> select add #2.7

486 atoms, 24 residues, 2 models selected  

> show sel atoms

> select subtract #2.7

243 atoms, 12 residues, 3 models selected  

> select subtract #2.8

1 model selected  
Drag select of 7 residues, 7 shapes  

> select subtract #2.8

81 atoms, 6 residues, 4 models selected  

> select subtract #2.7

21 atoms, 3 residues, 3 models selected  

> select add #2.9

264 atoms, 15 residues, 2 models selected  

> select add #2.10

507 atoms, 27 residues, 3 models selected  

> show sel cartoons

> hide sel cartoons

> save /Users/kompa012/Desktop/P53/2ac0.png width 3000 height 2520 supersample
> 3 transparentBackground true

Cell requested for row 11 is out of bounds for table with 29 rows! Resizing
table model.  

> show #!4 models

> hide #!2 models

> show #!2 models

> show #!5 models

> hide #!4 models

> hide #!5 models

> show #!4 models

> show #!5 models

> select add #2

8210 atoms, 7408 bonds, 78 pseudobonds, 1896 residues, 6 models selected  

> select subtract #2

8 models selected  

> hide #!4 models

> hide #!5 models

> show #!5 models

> show #!4 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!5 models

> hide #!4 models

> show #!4 models

> show #!5 models

> show #!2 models

> hide #!4 models

> hide #!5 models

> show #!4 models

> hide #!2 models

> save /Users/kompa012/Desktop/P53/2ahi.png width 3000 height 2520 supersample
> 3 transparentBackground true

> hide #!4 models

> show #!4 models

> show #!5 models

> hide #!4 models

> show #!6 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!6 models

> show #!18 models

> hide #!18 models

> show #!17 models

> hide #!17 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!15 models

> hide #!15 models

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!12 models

> hide #!12 models

> show #!11 models

> hide #!11 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!16 models

> show #!15 models

> show #!14 models

> hide #!15 models

> hide #!16 models

> show #!19 models

> hide #!14 models

> save /Users/kompa012/Desktop/P53/3d0a.png width 3000 height 2520 supersample
> 3 transparentBackground true

> hide #!19 models

> show #!18 models

> show #!17 models

> hide #!17 models

> hide #!18 models

> show #!18 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!18 models

> show #!18 models

> hide #!17 models

> show #!17 models

> hide #!18 models

> show #!18 models

> hide #!17 models

> show #!17 models

> hide #!18 models

> show #!18 models

> hide #!17 models

> show #!17 models

> hide #!18 models

> hide #!17 models

> show #!17 models

> show #!18 models

> hide #!17 models

> save /Users/kompa012/Desktop/P53/3q06.png width 3000 height 2520 supersample
> 3 transparentBackground true

> show #!17 models

> hide #!18 models

> save /Users/kompa012/Desktop/P53/3q05.png width 3000 height 2520 supersample
> 3 transparentBackground true

> hide #!17 models

> show #!16 models

> select add #16.5

410 atoms, 20 residues, 1 model selected  

> select subtract #16.5

1 model selected  

> select add #16.4

1486 atoms, 195 residues, 1 model selected  

> select subtract #16.4

1 model selected  

> select add #16.3

1486 atoms, 195 residues, 1 model selected  

> select subtract #16.3

1 model selected  

> show #!15 models

> hide #!15 models

> show #!19 models

> hide #!19 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> open /Users/kompa012/Desktop/P53/3kz8.pdb1

3kz8.pdb1 title:  
Diversity In DNA recognition by P53 revealed by crystal structures with
hoogsteen base pairs (P53-DNA complex 3) [more info...]  
  
87 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Chain information for 3kz8.pdb1  
---  
Chain | Description  
20.1/A 20.1/B | No description available  
20.2/A 20.2/B | No description available  
20.1/C | No description available  
20.2/C | No description available  
  
87 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

> matchmaker #20.1/A to #12/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain A (#12) with 3kz8.pdb1, chain A (#20.1), sequence
alignment score = 948.3  
RMSD between 180 pruned atom pairs is 0.603 angstroms; (across all 195 pairs:
2.497)  
  

> matchmaker #20.2/A to #12/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain B (#12) with 3kz8.pdb1, chain A (#20.2), sequence
alignment score = 882.9  
RMSD between 180 pruned atom pairs is 0.876 angstroms; (across all 195 pairs:
1.248)  
  

> matchmaker #20.2/B to #12/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain B (#12) with 3kz8.pdb1, chain B (#20.2), sequence
alignment score = 891.9  
RMSD between 180 pruned atom pairs is 0.881 angstroms; (across all 195 pairs:
1.263)  
  

> show #!12 models

> matchmaker #20.1/C to #12/K pairing ss

Using Nucleic matrix instead of BLOSUM-62 to match 3kz8.pdb1 #20.1/C to 3ts8
#12/K  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain K (#12) with 3kz8.pdb1, chain C (#20.1), sequence
alignment score = 33.8  
RMSD between 16 pruned atom pairs is 1.144 angstroms; (across all 20 pairs:
1.781)  
  

> matchmaker #20.2/C to #12/K pairing ss

Using Nucleic matrix instead of BLOSUM-62 to match 3kz8.pdb1 #20.2/C to 3ts8
#12/K  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain K (#12) with 3kz8.pdb1, chain C (#20.2), sequence
alignment score = 35.9  
RMSD between 16 pruned atom pairs is 1.144 angstroms; (across all 20 pairs:
1.781)  
  

> matchmaker #20.1/C to #12/L pairing ss

Using Nucleic matrix instead of BLOSUM-62 to match 3kz8.pdb1 #20.1/C to 3ts8
#12/L  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain L (#12) with 3kz8.pdb1, chain C (#20.1), sequence
alignment score = 38.7  
RMSD between 17 pruned atom pairs is 1.147 angstroms; (across all 20 pairs:
1.783)  
  

> hide #!12 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!12 models

> hide #!16 models

> hide #!20.1 models

> show #!20.1 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!12 models

> ui tool show "Crystal Contacts"

> show #!16 models

> hide #!20 models

> crystalcontacts #20.1 distance 8

11 pairs of asymmetric units of 3kz8.pdb1 contact at distance 8.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
       961     0      1      0  0  1      0         1
       437     0      3      0  0  1      0         1
       298     0      3      0 -1  1      0         1
       222     0      0      0  0 -1      0         1
       172     0      0      0  0  1      0         1
        59     0      0      0  1  0      0         1
        56     0      0      0 -1  0      0         1
        35     0      1      0  0  2      0         1
        34     0      1      0  0  0      0         1
         9     0      3      0 -1  0      0         1
         7     0      3      0  0  0      0         1
    

  

> select add #21

40667 atoms, 38489 bonds, 110 pseudobonds, 7975 residues, 34 models selected  

> show sel atoms

> show sel cartoons

> show sel surfaces

> crystalcontacts #20.1 distance 4

9 pairs of asymmetric units of 3kz8.pdb1 contact at distance 4.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
       321     0      1      0  0  1      0         1
        67     0      3      0  0  1      0         1
        66     0      3      0 -1  1      0         1
        43     0      0      0  0 -1      0         1
        41     0      0      0  0  1      0         1
        18     0      0      0  1  0      0         1
        11     0      0      0 -1  0      0         1
         3     0      1      0  0  2      0         1
         3     0      1      0  0  0      0         1
    

  

> select clear

> select add #20

7394 atoms, 6998 bonds, 12 pseudobonds, 1450 residues, 6 models selected  

> show #!20 models

> close #20

> select add #21.9

3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 3 models selected  

> select add #21.8

7394 atoms, 6998 bonds, 20 pseudobonds, 1450 residues, 6 models selected  

> select add #21.7

11091 atoms, 10497 bonds, 30 pseudobonds, 2175 residues, 9 models selected  

> select add #21.6

14788 atoms, 13996 bonds, 40 pseudobonds, 2900 residues, 12 models selected  

> select add #21.5

18485 atoms, 17495 bonds, 50 pseudobonds, 3625 residues, 15 models selected  

> select add #21.4

22182 atoms, 20994 bonds, 60 pseudobonds, 4350 residues, 18 models selected  

> select add #21.3

25879 atoms, 24493 bonds, 70 pseudobonds, 5075 residues, 21 models selected  

> hide sel atoms

> hide sel cartoons

> select add #21.2

29576 atoms, 27992 bonds, 80 pseudobonds, 5800 residues, 24 models selected  

> hide sel atoms

> hide sel cartoons

> select add #21.1

33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 27 models selected  

> select add #21

33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 28 models selected  

> select subtract #21

Nothing selected  

> select add #21.1

3697 atoms, 3499 bonds, 10 pseudobonds, 725 residues, 3 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #21.1.5

3287 atoms, 3040 bonds, 10 pseudobonds, 705 residues, 6 models selected  

> hide sel cartoons

> hide sel atoms

Drag select of 92 atoms, 101 bonds, 7 residues  

> hide sel atoms

> hide sel cartoons

> select subtract #21.1.5

1 model selected  

> select add #21.1.5

410 atoms, 20 residues, 1 model selected  

> nucleotides sel tube/slab shape box

Drag select of 27 atoms, 221 residues, 1 pseudobonds, 78 shapes  

> show #!15 models

> show #!14 models

> show #!2 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> select add #16

3959 atoms, 3499 bonds, 10 pseudobonds, 738 residues, 7 models selected  

> select subtract #16

262 atoms, 13 residues, 5 models selected  

> select add #21

33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 29 models selected  

> select subtract #21

3 models selected  

> select add #21.1.3

1486 atoms, 195 residues, 1 model selected  

> select add #21.1.5

1896 atoms, 215 residues, 2 models selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!16 models

> select add #21

33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 30 models selected  

> show #!15 models

> hide #!21 models

> hide #!16 models

> show #!14 models

> hide #!14 models

> hide #!15 models

> select subtract #21

3 models selected  

> show #!15 models

> show #!14 models

> show #!13 models

> hide #!13 models

> show #!12 models

> hide #!12 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!14 models

> hide #!15 models

> hide #!11 models

> show #!11 models

> show #!21 models

> show #!16 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> select add #21

33273 atoms, 31491 bonds, 90 pseudobonds, 6525 residues, 28 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.98958,0.012409,-0.14344,0.91941,-0.039208,0.98185,-0.18555,1.6593,0.13854,0.18924,0.97211,-2.389

> hide #!11 models

> view matrix models
> #21,0.98313,0.082637,-0.16316,0.71163,-0.11628,0.97101,-0.20883,2.6873,0.14117,0.22428,0.96425,-2.5673

> view matrix models
> #21,0.98538,0.07809,-0.15144,0.64248,-0.10827,0.97326,-0.20261,2.5513,0.13157,0.21604,0.96748,-2.4375

> show #!2 models

> hide #!16 models

> hide #!21 models

> ui mousemode right select

> select clear

> show #!19 models

> hide #!19 models

> hide #!2 models

> show #!21 models

> show #!16 models

> show #!15 models

> show #!14 models

> hide #!21 models

> hide #!16 models

> ui tool show "Crystal Contacts"

> crystalcontacts #15 distance 4

10 pairs of asymmetric units of 3igl contact at distance 4.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
       201     0      1      0  0  2      0         1
        99     0      0      0  0  1      0         1
        86     0      0      0  0 -1      0         1
        80     0      3      0  0  2      0         1
        65     0      3      0 -1  2      0         1
        21     0      1      0  0  1      0         1
        12     0      0      0  1  0      0         1
         9     0      0      0 -1  0      0         1
         1     0      3      0  0  1      0         1
         1     0      3      0 -1  1      0         1
    

  

> crystalcontacts #14 distance 4

10 pairs of asymmetric units of 3igk contact at distance 4.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
       174     0      1      0  0  2      0         1
       101     0      0      0  0 -1      0         1
        86     0      0      0  0  1      0         1
        72     0      3      0 -1  2      0         1
        64     0      3      0  0  2      0         1
        22     0      1      0  0  1      0         1
        12     0      0      0  1  0      0         1
         9     0      0      0 -1  0      0         1
         3     0      3      0  0  1      0         1
         1     0      3      0 -1  1      0         1
    

  

> hide #!22 models

> hide #!20 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!14 models

> show #!14 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!15 models

> hide #!14 models

> show #!13 models

> hide #!16 models

> show #!7 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> hide #!7 models

> show #!10 models

> show #!9 models

> show #!8 models

> hide #!9 models

> hide #!10 models

> show #!10 models

> show #!9 models

> hide #!9 models

> hide #!10 models

> show #!9 models

> hide #!8 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #!9 models

> show #!8 models

> show #!11 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!6 models

> show #!3 models

> hide #!11 models

> hide #!6 models

> show #!6 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!6 models

> ui tool show Matchmaker

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!2 models

> save /Users/kompa012/Desktop/P53/5lgy.png width 3000 height 2520 supersample
> 3 transparentBackground true

> show #!18 models

> hide #!3 models

> show #!17 models

> hide #!18 models

> show #!18 models

> hide #!17 models

> show #!17 models

> hide #!18 models

> hide #!17 models

> show #!16 models

> show #!21 models

> save /Users/kompa012/Desktop/P53/3kz8.png width 3000 height 2520 supersample
> 3 transparentBackground true

> hide #!16 models

> hide #!21 models

> show #!13 models

Drag select of 11 atoms, 11 bonds  

> hide sel atoms

Drag select of 1 atoms  

> hide sel atoms

> save /Users/kompa012/Desktop/P53/3kmd.png width 3000 height 2520 supersample
> 3 transparentBackground true

> hide #!13 models

> select add #13

7587 atoms, 7298 bonds, 64 pseudobonds, 1365 residues, 3 models selected  

> select subtract #13

6 models selected  

> show #!12 models

> save /Users/kompa012/Desktop/P53/3ts8.png width 3000 height 2520 supersample
> 3 transparentBackground true

> show #!7 models

> hide #!12 models

> save /Users/kompa012/Desktop/P53/4mzr.png width 3000 height 2520 supersample
> 3 transparentBackground true

> hide #!7 models

> show #!8 models

> save /Users/kompa012/Desktop/P53/4ibu.png width 3000 height 2520 supersample
> 3 transparentBackground true

> save "/Users/kompa012/Desktop/P53/Before mutation.cxs"

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> show #!13 models

> hide #!12 models

> hide #!13 models

> show #!14 models

> show #!13 models

> show #!12 models

> show #!15 models

> show #!16 models

> show #!17 models

> show #!18 models

> show #!19 models

> open 6shz fromDatabase pdb format mmcif

Summary of feedback from opening 6shz fetched from pdb  
---  
note | Fetching compressed mmCIF 6shz from http://files.rcsb.org/download/6shz.cif  
  
6shz title:  
p53 cancer mutant Y220C [more info...]  
  
Chain information for 6shz #23  
---  
Chain | Description | UniProt  
A B | Cellular tumor antigen p53 | P53_HUMAN 94-311  
  
Non-standard residues in 6shz #23  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
ZN — zinc ion  
  
6shz mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
134 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open 2J1x fromDatabase pdb format mmcif

Summary of feedback from opening 2J1x fetched from pdb  
---  
note | Fetching compressed mmCIF 2j1x from http://files.rcsb.org/download/2j1x.cif  
  
2j1x title:  
Human p53 core domain mutant M133L-V203A-Y220C-N239Y-N268D [more info...]  
  
Chain information for 2j1x #24  
---  
Chain | Description | UniProt  
A B | CELLULAR TUMOR ANTIGEN P53 | P53_HUMAN 94-312  
  
Non-standard residues in 2j1x #24  
---  
ZN — zinc ion  
  
2j1x mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open 1uol fromDatabase pdb format mmcif

Summary of feedback from opening 1uol fetched from pdb  
---  
note | Fetching compressed mmCIF 1uol from http://files.rcsb.org/download/1uol.cif  
  
1uol title:  
Crystal structure of the human p53 core domain mutant M133L/V203A/N239Y/N268D
at 1.9 A resolution. [more info...]  
  
Chain information for 1uol #25  
---  
Chain | Description | UniProt  
A B | CELLULAR TUMOR ANTIGEN P53 | P53_HUMAN 94-312  
  
Non-standard residues in 1uol #25  
---  
ZN — zinc ion  
  
1uol mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> hide #!18 models

> hide #!19 models

> open 8a32 fromDatabase pdb format mmcif

Summary of feedback from opening 8a32 fetched from pdb  
---  
note | Fetching compressed mmCIF 8a32 from http://files.rcsb.org/download/8a32.cif  
  
8a32 title:  
p53 cancer mutant Y220C in complex with iodophenol-based small-molecule
stabilizer JC769 [more info...]  
  
Chain information for 8a32 #26  
---  
Chain | Description | UniProt  
A B | Cellular tumor antigen p53 | P53_HUMAN 94-312  
  
Non-standard residues in 8a32 #26  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
KVA — 4-[3,4-bis(fluoranyl)pyrrol-1-yl]-3,5-bis(iodanyl)-2-oxidanyl-benzoic
acid  
ZN — zinc ion  
  
8a32 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
102 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

> matchmaker #25/A to #12/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain A (#12) with 1uol, chain A (#25), sequence alignment
score = 927.9  
RMSD between 187 pruned atom pairs is 0.575 angstroms; (across all 195 pairs:
2.313)  
  

> matchmaker #25/B to #12/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain A (#12) with 1uol, chain B (#25), sequence alignment
score = 927.9  
RMSD between 186 pruned atom pairs is 0.585 angstroms; (across all 195 pairs:
2.289)  
  

> matchmaker #25/A to #12/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain A (#12) with 1uol, chain A (#25), sequence alignment
score = 927.9  
RMSD between 187 pruned atom pairs is 0.575 angstroms; (across all 195 pairs:
2.313)  
  

> matchmaker #24/A to #12/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain A (#12) with 2j1x, chain A (#24), sequence alignment
score = 909.6  
RMSD between 187 pruned atom pairs is 0.557 angstroms; (across all 195 pairs:
2.329)  
  

> matchmaker #23/A to #12/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain A (#12) with 6shz, chain A (#23), sequence alignment
score = 916.9  
RMSD between 189 pruned atom pairs is 0.550 angstroms; (across all 197 pairs:
2.279)  
  

> matchmaker #26/A to #12/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ts8, chain A (#12) with 8a32, chain A (#26), sequence alignment
score = 916.2  
RMSD between 189 pruned atom pairs is 0.590 angstroms; (across all 197 pairs:
2.303)  
  

> hide #!12 models

> matchmaker #25/A to #24/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2j1x, chain A (#24) with 1uol, chain A (#25), sequence alignment
score = 1098.9  
RMSD between 195 pruned atom pairs is 0.170 angstroms; (across all 195 pairs:
0.170)  
  

> hide #!23 models

> hide #!26 models

> ui tool show "Show Sequence Viewer"

> sequence chain #24/A

Alignment identifier is 24/A  

> sequence chain #25/A

Alignment identifier is 25/A  

> sequence chain #26/A

Alignment identifier is 26/A  

> sequence chain #23/A

Alignment identifier is 23/A  

> select #25/A:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #25/A:220-221

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select #25/A:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #25/A:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select add #25

3465 atoms, 3144 bonds, 8 pseudobonds, 783 residues, 2 models selected  

> color (#!25 & sel) dark gray

> select subtract #25

Nothing selected  

> select add #24

3459 atoms, 3133 bonds, 8 pseudobonds, 786 residues, 2 models selected  

> color (#!24 & sel) yellow

> select add #26

6990 atoms, 6292 bonds, 16 pseudobonds, 1628 residues, 4 models selected  

> select subtract #24

3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 2 models selected  

> show #!26 models

> color (#!26 & sel) orange

> color (#!26 & sel) red

> select add #23

7103 atoms, 6283 bonds, 16 pseudobonds, 1755 residues, 4 models selected  

> select subtract #26

3572 atoms, 3124 bonds, 8 pseudobonds, 913 residues, 2 models selected  

> show #!23 models

> color (#!23 & sel) forest green

> select add #24

7031 atoms, 6257 bonds, 16 pseudobonds, 1699 residues, 4 models selected  

> select add #26

10562 atoms, 9416 bonds, 24 pseudobonds, 2541 residues, 6 models selected  

> select add #25

14027 atoms, 12560 bonds, 32 pseudobonds, 3324 residues, 8 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #23

10455 atoms, 9436 bonds, 24 pseudobonds, 2411 residues, 14 models selected  

> select add #23.3

11975 atoms, 9436 bonds, 24 pseudobonds, 2609 residues, 13 models selected  

> hide sel cartoons

> select subtract #23.3

10455 atoms, 9436 bonds, 24 pseudobonds, 2411 residues, 13 models selected  

> select add #23.2

11978 atoms, 9436 bonds, 24 pseudobonds, 2608 residues, 13 models selected  

> select subtract #23.2

10455 atoms, 9436 bonds, 24 pseudobonds, 2411 residues, 13 models selected  

> select subtract #24.3

8922 atoms, 7868 bonds, 20 pseudobonds, 2216 residues, 12 models selected  

> select add #24.3

10455 atoms, 7868 bonds, 20 pseudobonds, 2411 residues, 11 models selected  

> select subtract #24.2

8925 atoms, 6303 bonds, 16 pseudobonds, 2216 residues, 11 models selected  

> select subtract #24.3

7392 atoms, 6303 bonds, 16 pseudobonds, 2021 residues, 10 models selected  

> select add #24.3

8925 atoms, 6303 bonds, 16 pseudobonds, 2216 residues, 9 models selected  

> select subtract #25

5460 atoms, 3159 bonds, 8 pseudobonds, 1433 residues, 8 models selected  

> select subtract #26

1929 atoms, 591 residues, 4 models selected  

> select subtract #24.3

396 atoms, 396 residues, 2 models selected  

> select add #24.3

1929 atoms, 591 residues, 1 model selected  

> select subtract #24.3

396 atoms, 396 residues, 2 models selected  

> select add #24.2

1926 atoms, 591 residues, 1 model selected  

> show sel cartoons

> select subtract #24.2

396 atoms, 396 residues, 2 models selected  

> select add #24.2

1926 atoms, 591 residues, 1 model selected  

> select subtract #24.2

396 atoms, 396 residues, 2 models selected  

> select add #24

3459 atoms, 3133 bonds, 8 pseudobonds, 786 residues, 2 models selected  

> select subtract #24

2 models selected  

> select add #25.2

1536 atoms, 195 residues, 1 model selected  

> show sel cartoons

> select add #25

3465 atoms, 3144 bonds, 8 pseudobonds, 783 residues, 3 models selected  

> select subtract #25

2 models selected  

> select add #26.2

1521 atoms, 197 residues, 1 model selected  

> show sel cartoons

> select add #26

3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 3 models selected  

> select subtract #26

2 models selected  
Drag select of 277 atoms, 16 pseudobonds, 244 bonds  

> hide sel atoms

> select #25/A:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #25/A:220

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #23-26 /A :220

30 atoms, 27 bonds, 4 residues, 4 models selected  

> show sel atoms

> hide #!25 models

> hide #!24 models

> hide #!23 models

> show #!11 models

> hide #!26 models

> select add #23

3596 atoms, 3146 bonds, 8 pseudobonds, 916 residues, 9 models selected  

> select subtract #23

24 atoms, 22 bonds, 3 residues, 8 models selected  

> select add #23

3596 atoms, 3146 bonds, 8 pseudobonds, 916 residues, 8 models selected  

> select subtract #23

24 atoms, 22 bonds, 3 residues, 8 models selected  

> select add #24

3477 atoms, 3150 bonds, 8 pseudobonds, 788 residues, 7 models selected  

> select subtract #24

18 atoms, 17 bonds, 2 residues, 6 models selected  

> select add #25

3471 atoms, 3149 bonds, 8 pseudobonds, 784 residues, 5 models selected  

> select subtract #25

6 atoms, 5 bonds, 1 residue, 4 models selected  

> select add #26

3531 atoms, 3159 bonds, 8 pseudobonds, 842 residues, 3 models selected  

> select subtract #26

2 models selected  

> save "/Users/kompa012/Desktop/P53/Y220C mutation.cxs"

> open "/Users/kompa012/Desktop/P53/Before mutation.cxs"

opened ChimeraX session  

> show #!11 models

> hide #!8 models

> save /Users/kompa012/Desktop/P53/4hje.png width 3000 height 2520 supersample
> 3 transparentBackground true

> open "/Users/kompa012/Desktop/P53/Y220C mutation.cxs"

opened ChimeraX session  

> hide #!11 models

> show #!25 models

> show #!24 models

> show #!26 models

> hide #!26 models

> show #!23 models

> show #!26 models

> hide #!25 models

> hide #!26 models

> show #!25 models

> hide #!23 models

> show #!26 models

> hide #!24 models

> hide #!26 models

> select #23-26 /A :151

28 atoms, 28 bonds, 4 residues, 4 models selected  

> show sel & #!25 atoms

> select #23-26 /A :153

28 atoms, 28 bonds, 4 residues, 4 models selected  

> show sel & #!25 atoms

> hide sel & #!25 atoms

> select #23-26 /A :155

28 atoms, 24 bonds, 4 residues, 4 models selected  

> show sel & #!25 atoms

> select #23-26 /A :222

28 atoms, 28 bonds, 4 residues, 4 models selected  

> show sel & #!25 atoms

> select #23-26 /A :220, 222, 153

86 atoms, 83 bonds, 12 residues, 4 models selected  

> select #23-26 /A :220, 222, 151

86 atoms, 83 bonds, 12 residues, 4 models selected  

> color (#!25 & sel) black

> select #23-26 /A :223

28 atoms, 28 bonds, 4 residues, 4 models selected  

> show sel & #!25 atoms

> hide sel & #!25 cartoons

> show sel & #!25 cartoons

> hide sel & #!25 atoms

> select #23-26 /A :145

32 atoms, 28 bonds, 4 residues, 4 models selected  

> show sel & #!25 atoms

> select #23-26 /A :223

28 atoms, 28 bonds, 4 residues, 4 models selected  

> show sel & #!25 atoms

> select #23-26 /A :147

28 atoms, 24 bonds, 4 residues, 4 models selected  

> show sel & #!25 atoms

> select ~sel & ##selected

13999 atoms, 12536 bonds, 32 pseudobonds, 3320 residues, 8 models selected  

> select #23-26 /A :151,153,155

84 atoms, 80 bonds, 12 residues, 4 models selected  

> show sel & #!25 atoms

> select #23-26 /A :151,153,155,223,220,147

170 atoms, 159 bonds, 24 residues, 4 models selected  

> show sel & #!25 cartoons

> show sel & #!25 atoms

> select #23-26 /A :222

28 atoms, 28 bonds, 4 residues, 4 models selected  

> hide sel & #!25 atoms

> color (#!25 & sel) light gray

> color (#!25 & sel) dark gray

> select #23-26 /A :151,153,155,223,220,147

170 atoms, 159 bonds, 24 residues, 4 models selected  

> color (#!25 & sel) black

> ui tool show H-Bonds

> save "/Users/kompa012/Desktop/P53/Y220C mutation.cxs"

> ui tool show H-Bonds

> hbonds sel reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 3d0a #19/F DG 4 O4'; 2ac0 #2/A LYS 292 N; 2ata #5/C LYS 291 N;
2ahi #4/A GLY 293 N; 2ata #5/B LYS 292 N; 2ata #5/D LYS 291 N; 3d0a #19/B PRO
153 N; 3d0a #19/D ARG 110 NE; 3d0a #19/D ARG 283 NE  

1055 hydrogen bonds found  

> show #!26 models

> show #!24 models

> show #!23 models

> show #!19 models

> hide #!19 models


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16S0005DLL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 13 days, 10 hours, 51 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (1)

comment:1 by Eric Pettersen, 7 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep
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