Opened 7 months ago

Closed 7 months ago

#17097 closed defect (duplicate)

Crash on Mac waking from sleep

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 

The following bug report has been submitted:
Platform:        macOS-14.6.1-x86_64-i386-64bit
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 0x0000700022eaa000 (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 0x0000700021ea7000 (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 0x0000700020ea4000 (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 0x000070001fea1000 (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 0x000070001ee9e000 (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 0x000070001de9b000 (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 0x000070001ce98000 (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 0x000070001be95000 (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 0x000070001ae92000 (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 0x0000700019e8f000 (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 0x0000700018e8c000 (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 0x0000700017e89000 (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 0x0000700016e86000 (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 0x0000700015e83000 (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 0x0000700014e80000 (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 0x0000700013e7d000 (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 0x0000700012e7a000 (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 0x0000700011e77000 (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 0x0000700010e74000 (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 0x000070000fe71000 (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 0x000070000ee6e000 (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 0x000070000de6b000 (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 0x000070000ce68000 (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 0x00007ff84b3d9dc0 (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, 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.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 59)


{"app_name":"ChimeraX","timestamp":"2025-03-14 09:34:28.00 -0500","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"FEFC352A-D536-4652-8C76-4DCD1A433D16"}
{
  "uptime" : 81000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "iMac20,1",
  "coalitionID" : 2491,
  "osVersion" : {
    "train" : "macOS 14.6.1",
    "build" : "23G93",
    "releaseType" : "User"
  },
  "captureTime" : "2025-03-14 09:34:25.9136 -0500",
  "codeSigningMonitor" : 0,
  "incident" : "FEFC352A-D536-4652-8C76-4DCD1A433D16",
  "pid" : 6107,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-03-13 13:29:16.4058 -0500",
  "procStartAbsTime" : 9171785487785,
  "procExitAbsTime" : 81478915978621,
  "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":"768DA260-76C1-5EB4-92DC-36F31D4684AE","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D77CBDCE-560E-A76E-6409-11E87F8970FF",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "bridgeVersion" : {"build":"21P6074","train":"8.6"},
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4530266112\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10e066000-10e06a000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":6107},
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4530266112\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10e066000-10e06a000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "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},
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/ksinha01/Kinases_local/FGFR1/pdbs/fgfr1_struc_nmr.cxs

Log from Thu Mar 13 10:39:34 2025

> alias dd distance delete

> alias rd ui mousemode right distance

> alias rs ui mousemode right select

> alias nmr1 hide #1.2-20 models

> alias slall label sel text
> "{0.label_one_letter_code}{0.number}{0.insertion_code}"

> alias lmearo label #1:thr,met,ala,leu,val,ile,phe,tyr text
> "{0.label_one_letter_code}{0.number}{0.insertion_code}"

> alias showbb show #1@N,C,CA,O,H; cartoon #1 suppress false; transparency #1
> 50 target c; hide #1:hoh

> alias hidebb hide #1@N,C,CA,O,H target a; transparency $1 0 target c

> alias sdist ui tool show Distances

> alias showmet show #1:ile,leu,val,met,ala,thr target a; hide H; color #1:ile
> paleturquoise target a; color #1:leu lightsalmon target a; color #1:val
> khaki target a; color #1:met thistle target a; color #1:ala yellowgreen
> target ab; color #1:thr aquamarine target a;color byhetero target a ; style
> #1 ball

> alias showmet2 show #2:ile,leu,val,met,ala,thr target a; hide H; color
> #2:ile paleturquoise target a; color #2:leu lightsalmon target a; color
> #2:val khaki target a; color #2:met thistle target a; color #2:ala
> yellowgreen target ab; color #2:thr aquamarine target a;color byhetero
> target a ; style #2 ball

> alias showmet3 show #3:ile,leu,val,met,ala,thr target a; hide H; color
> #3:ile paleturquoise target a; color #3:leu lightsalmon target a; color
> #3:val khaki target a; color #3:met thistle target a; color #3:ala
> yellowgreen target ab; color #3:thr aquamarine target a;color byhetero
> target a ; style #3 ball

> alias showaro show #1:phe,tyr,his,trp target ab; hide H; color #1:phe plum
> target a; color #1:tyr lightpink target a; color byhetero target a

> ui mousemode right distance

> alias fgfr1_brake show #1: 546,562,638

> alias fgfr2_brake show #1: 549,565,641

> alias fgfr3_brake show #1: 540,556,632

> alias fgfr4_brake show #1: 535,551,627

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/ksinha01/Kinases_local/FGFR1/FGFR1_struc_calc/fgfr1_040_4_brake_2_072_v13_082823/final.pdb

Chain information for final.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | No description available  
  

> hide #1.2-20 cartoons

> hide #1.2-20

> showmet

Changed 98240 atom styles  

> hide #1.2-20

> set bgColor white

> label #1.1: 498

> distance #1.1/A:498@CD1 #1.1/A:508@CG1

Distance between final.pdb #1.1/A ILE 498 CD1 and VAL 508 CG1: 3.377Å  

> distance #1.1/A:498@CD1 #1.1/A:479@CG2

Distance between final.pdb #1.1/A ILE 498 CD1 and VAL 479 CG2: 5.271Å  

> distance #1.1/A:479@CG1 #1.1/A:498@CD1

Distance between final.pdb #1.1/A VAL 479 CG1 and ILE 498 CD1: 6.506Å  

> distance #1.1/A:498@CD1 #1.1/A:508@CG2

Distance between final.pdb #1.1/A ILE 498 CD1 and VAL 508 CG2: 3.465Å  

> label #1.1: 498,478

> label #1.1: 651

> distance #1.1/A:672@CD2 #1.1/A:651@CD1

Distance between final.pdb #1.1/A LEU 672 CD2 and ILE 651 CD1: 4.103Å  

> distance #1.1/A:651@CD1 #1.1/A:664@CG1

Distance between final.pdb #1.1/A ILE 651 CD1 and VAL 664 CG1: 5.547Å  

> distance #1.1/A:651@CD1 #1.1/A:667@CE

Distance between final.pdb #1.1/A ILE 651 CD1 and MET 667 CE: 5.814Å  

> ~distance #1.1/A:672@CD2 #1.1/A:651@CD1

> ~distance #1.1/A:651@CD1 #1.1/A:667@CE

> label #1.1: 651,493

> ~distance #1.1/A:651@CD1 #1.1/A:664@CG1

> distance #1.1/A:713@CD1 #1.1/A:651@CD1

Distance between final.pdb #1.1/A LEU 713 CD1 and ILE 651 CD1: 8.583Å  

> ~distance #1.1/A:713@CD1 #1.1/A:651@CD1

> label #1.1: 651,493,529

> distance #1.1/A:532@CE #1.1/A:529@CD1

Distance between final.pdb #1.1/A MET 532 CE and ILE 529 CD1: 5.029Å  

> distance #1.1/A:465@CD1 #1.1/A:529@CD1

Distance between final.pdb #1.1/A LEU 465 CD1 and ILE 529 CD1: 3.137Å  

> distance #1.1/A:529@CD1 #1.1/A:557@CD2

Distance between final.pdb #1.1/A ILE 529 CD1 and LEU 557 CD2: 3.651Å  

> distance #1.1/A:529@CD1 #1.1/A:528@CD2

Distance between final.pdb #1.1/A ILE 529 CD1 and LEU 528 CD2: 5.098Å  

> distance #1.1/A:529@CD1 #1.1/A:525@CD1

Distance between final.pdb #1.1/A ILE 529 CD1 and LEU 525 CD1: 3.179Å  

> distance #1.1/A:529@CD1 #1.1/A:516@CD1

Distance between final.pdb #1.1/A ILE 529 CD1 and LEU 516 CD1: 5.532Å  

> distance #1.1/A:552@CG2 #1.1/A:529@CD1

Distance between final.pdb #1.1/A THR 552 CG2 and ILE 529 CD1: 7.477Å  

> distance #1.1/A:532@CE #1.1/A:552@CG2

Distance between final.pdb #1.1/A MET 532 CE and THR 552 CG2: 4.591Å  

> ~distance #1.1/A:552@CG2 #1.1/A:529@CD1

> ~distance #1.1/A:532@CE #1.1/A:529@CD1

> ~distance #1.1/A:465@CD1 #1.1/A:529@CD1

> label #1.1: 651,493,631

> label #1.1: 651,493,631,479

> ~distance #1.1/A:529@CD1 #1.1/A:557@CD2

> ~distance #1.1/A:529@CD1 #1.1/A:516@CD1

> ~distance #1.1/A:529@CD1 #1.1/A:528@CD2

> ~distance #1.1/A:529@CD1 #1.1/A:525@CD1

> label #1.1: 651,493,631,479,693

> distance #1.1/A:693@CD1 #1.1/A:689@CD2

Distance between final.pdb #1.1/A ILE 693 CD1 and LEU 689 CD2: 4.294Å  

> distance #1.1/A:693@CD1 #1.1/A:690@CD2

Distance between final.pdb #1.1/A ILE 693 CD1 and LEU 690 CD2: 5.279Å  

> distance #1.1/A:693@CD1 #1.1/A:569@CD2

Distance between final.pdb #1.1/A ILE 693 CD1 and LEU 569 CD2: 4.038Å  

> distance #1.1/A:693@CD1 #1.1/A:595@CD1

Distance between final.pdb #1.1/A ILE 693 CD1 and LEU 595 CD1: 9.545Å  

> ~distance #1.1/A:693@CD1 #1.1/A:595@CD1

> distance #1.1/A:637@CE #1.1/A:693@CD1

Distance between final.pdb #1.1/A MET 637 CE and ILE 693 CD1: 5.340Å  

> distance #1.1/A:604@CB #1.1/A:693@CD1

Distance between final.pdb #1.1/A ALA 604 CB and ILE 693 CD1: 4.380Å  

> distance #1.1/A:693@CD1 #1.1/A:607@CG2

Distance between final.pdb #1.1/A ILE 693 CD1 and VAL 607 CG2: 4.552Å  

> ~distance #1.1/A:604@CB #1.1/A:693@CD1

> ~distance #1.1/A:693@CD1 #1.1/A:607@CG2

> ~distance #1.1/A:637@CE #1.1/A:693@CD1

> hide #1.2-20#!2 target m

> label #1.1: 521,657,658,493,624

> distance #1.1/A:639@CD1 #1.1/A:693@CD1

Distance between final.pdb #1.1/A ILE 639 CD1 and ILE 693 CD1: 9.000Å  

> distance #1.1/A:693@CD1 #1.1/A:639@CD1

Distance already exists; modify distance properties with 'distance style'  

> show #!2 models

> ~distance #1.1/A:639@CD1 #1.1/A:693@CD1

> ~label

> label #1.1: 706

> label #1.1: 706,651

> distance #1.1/A:706@CG1 #1.1/A:651@CD1

Distance between final.pdb #1.1/A VAL 706 CG1 and ILE 651 CD1: 7.471Å  

> distance #1.1/A:664@CG1 #1.1/A:651@CD1

Distance between final.pdb #1.1/A VAL 664 CG1 and ILE 651 CD1: 5.547Å  

> ~distance #1.1/A:706@CG1 #1.1/A:651@CD1

> distance #1.1/A:651@CD1 #1.1/A:709@CD2

Distance between final.pdb #1.1/A ILE 651 CD1 and LEU 709 CD2: 7.802Å  

> ~distance #1.1/A:651@CD1 #1.1/A:709@CD2

> distance #1.1/A:672@CD2 #1.1/A:651@CD1

Distance between final.pdb #1.1/A LEU 672 CD2 and ILE 651 CD1: 4.103Å  

> ~distance #1.1/A:672@CD2 #1.1/A:651@CD1

> distance #1.1/A:672@CD2 #1.1/A:651@CD1

Distance between final.pdb #1.1/A LEU 672 CD2 and ILE 651 CD1: 4.103Å  

> distance #1.1/A:667@CE #1.1/A:672@CD2

Distance between final.pdb #1.1/A MET 667 CE and LEU 672 CD2: 3.191Å  

> label #1.1: 706,651,657

> ~label

> label #1.1: 620

> distance #1.1/A:678@CG2 #1.1/A:620@CD1

Distance between final.pdb #1.1/A THR 678 CG2 and ILE 620 CD1: 5.652Å  

> label #1.1: 620,614

> label #1.1: 620,614,662

> ~label

> label #1.1: 560

> distance #1.1/A:560@CD1 #1.1/A:500@CD2

Distance between final.pdb #1.1/A ILE 560 CD1 and LEU 500 CD2: 5.520Å  

> distance #1.1/A:560@CD1 #1.1/A:478@CD2

Distance between final.pdb #1.1/A ILE 560 CD1 and LEU 478 CD2: 3.224Å  

> distance #1.1/A:560@CD1 #1.1/A:511@CG1

Distance between final.pdb #1.1/A ILE 560 CD1 and VAL 511 CG1: 5.731Å  

> distance #1.1/A:497@CB #1.1/A:560@CD1

Distance between final.pdb #1.1/A ALA 497 CB and ILE 560 CD1: 5.156Å  

> distance #1.1/A:560@CD1 #1.1/A:509@CG2

Distance between final.pdb #1.1/A ILE 560 CD1 and THR 509 CG2: 9.344Å  

> ~distance #1.1/A:560@CD1 #1.1/A:509@CG2

> distance #1.1/A:473@CD2 #1.1/A:560@CD1

Distance between final.pdb #1.1/A LEU 473 CD2 and ILE 560 CD1: 3.428Å  

> distance #1.1/A:548@CD1 #1.1/A:560@CD1

Distance between final.pdb #1.1/A LEU 548 CD1 and ILE 560 CD1: 7.353Å  

> ~distance #1.1/A:548@CD1 #1.1/A:560@CD1

> distance #1.1/A:560@CD1 #1.1/A:513@CG1

Distance between final.pdb #1.1/A ILE 560 CD1 and VAL 513 CG1: 5.569Å  

> label #1.1: 560,500,478,511,497,473,513,560

> label #1.1: 560,500,478,511,497,473,513,560,548

> distance #1.1/A:548@CD1 #1.1/A:560@CD1

Distance between final.pdb #1.1/A LEU 548 CD1 and ILE 560 CD1: 7.353Å  

> distance #1.1/A:548@CB #1.1/A:560@CD1

Distance between final.pdb #1.1/A LEU 548 CB and ILE 560 CD1: 5.998Å  

> ~distance #1.1/A:548@CD1 #1.1/A:560@CD1

> ~distance #1.1/A:498@CD1 #1.1/A:479@CG2

> label #1.1: 560,500,478,511,497,473,513,560,548,460

> ~distance #1.1/A:473@CD2 #1.1/A:560@CD1

> ~distance #1.1/A:560@CD1 #1.1/A:478@CD2

> ~label #1.1: 478,473

> ~distance #1.1/A:560@CD1 #1.1/A:513@CG1

> ~distance #1.1/A:560@CD1 #1.1/A:500@CD2

> ~distance #1.1/A:560@CD1 #1.1/A:511@CG1

> ~label

> label #1.1: 626

> ~distance #1.1/A:497@CB #1.1/A:560@CD1

> ~distance #1.1/A:548@CB #1.1/A:560@CD1

> ~distance #1.1/A:498@CD1 #1.1/A:508@CG1

> ~distance #1.1/A:479@CG1 #1.1/A:498@CD1

> ~distance #1.1/A:498@CD1 #1.1/A:508@CG2

> ~distance #1.1/A:693@CD1 #1.1/A:689@CD2

> ~distance #1.1/A:693@CD1 #1.1/A:569@CD2

> ~distance #1.1/A:693@CD1 #1.1/A:690@CD2

> distance #1.1/A:626@CB #1.1/A:693@CD1

Distance between final.pdb #1.1/A ALA 626 CB and ILE 693 CD1: 6.240Å  

> distance #1.1/A:626@CB #1.1/A:569@CD2

Distance between final.pdb #1.1/A ALA 626 CB and LEU 569 CD2: 3.655Å  

> ~distance #1.1/A:626@CB #1.1/A:693@CD1

> distance #1.1/A:626@CB #1.1/A:693@CD1

Distance between final.pdb #1.1/A ALA 626 CB and ILE 693 CD1: 6.240Å  

> distance #1.1/A:637@CE #1.1/A:626@CB

Distance between final.pdb #1.1/A MET 637 CE and ALA 626 CB: 6.865Å  

> ~distance #1.1/A:637@CE #1.1/A:626@CB

> distance #1.1/A:626@CB #1.1/A:689@CD1

Distance between final.pdb #1.1/A ALA 626 CB and LEU 689 CD1: 3.904Å  

> distance #1.1/A:607@CG2 #1.1/A:626@CB

Distance between final.pdb #1.1/A VAL 607 CG2 and ALA 626 CB: 7.870Å  

> ~distance #1.1/A:607@CG2 #1.1/A:626@CB

> distance #1.1/A:629@CG1 #1.1/A:626@CB

Distance between final.pdb #1.1/A VAL 629 CG1 and ALA 626 CB: 5.845Å  

> ~distance #1.1/A:629@CG1 #1.1/A:626@CB

> ~distance #1.1/A:626@CB #1.1/A:569@CD2

> ~distance #1.1/A:626@CB #1.1/A:693@CD1

> ~distance #1.1/A:626@CB #1.1/A:689@CD1

> show

> showmet

Changed 98240 atom styles  

> hide atoms

> showmet

Changed 98240 atom styles  

> show #1.1:653,654

> distance #1.1/A:626@CB #1.1/A:658@CG2

Distance between final.pdb #1.1/A ALA 626 CB and THR 658 CG2: 20.134Å  

> ~distance #1.1/A:626@CB #1.1/A:658@CG2

> label #1.1: 626,624

> distance #1.1/A:624@CD2 #1.1/A:626@CB

Distance between final.pdb #1.1/A LEU 624 CD2 and ALA 626 CB: 8.255Å  

> ~distance #1.1/A:624@CD2 #1.1/A:626@CB

> ~label

> label #1.1: 532

> distance #1.1/A:532@CE #1.1/A:465@CD1

Distance between final.pdb #1.1/A MET 532 CE and LEU 465 CD1: 3.298Å  

> distance #1.1/A:532@CE #1.1/A:529@CD1

Distance between final.pdb #1.1/A MET 532 CE and ILE 529 CD1: 5.029Å  

> distance #1.1/A:532@CE #1.1/A:557@CD1

Distance between final.pdb #1.1/A MET 532 CE and LEU 557 CD1: 3.647Å  

> distance #1.1/A:559@CG2 #1.1/A:532@CE

Distance between final.pdb #1.1/A VAL 559 CG2 and MET 532 CE: 3.490Å  

> distance #1.1/A:528@CD2 #1.1/A:532@CE

Distance between final.pdb #1.1/A LEU 528 CD2 and MET 532 CE: 5.929Å  

> ~distance #1.1/A:532@CE #1.1/A:529@CD1

> rota #1.1:535

rota is provided by the uninstalled bundle ISOLDE versions 1.7rc1 – 1.8  

> swappaa #1.1:535 MET

Unknown command: swappaa #1.1:535 MET  

> swapaa #1.1:535 MET

Using Dunbrack library  
final.pdb #1.1/A MET 535: phi -55.0, psi -33.6 trans  
Applying MET rotamer (chi angles: -178.6 179.7 71.4) to final.pdb #1.1/A MET
535  

> swapaa interactive #1.1:535 MET

final.pdb #1.1/A MET 535: phi -55.0, psi -33.6 trans  
Changed 135 bond radii  

> ~distance #1.1/A:532@CE #1.1/A:552@CG2

> ~distance #1.1/A:532@CE #1.1/A:465@CD1

> save /Users/ksinha01/Kinases_local/FGFR1/pdbs/fgfr1_struc_nmr.cxs

——— End of log from Thu Mar 13 10:39:34 2025 ———

opened ChimeraX session  

> ~distance #1.1/A:532@CE #1.1/A:557@CD1

> ~distance #1.1/A:559@CG2 #1.1/A:532@CE

> ~label

> label #1.1: 534

> ~distance #1.1/A:528@CD2 #1.1/A:532@CE

> distance #1.1/A:537@CE #1.1/A:534@CE

Distance between final.pdb #1.1/A MET 537 CE and MET 534 CE: 3.712Å  

> distance #1.1/A:538@CD1 #1.1/A:534@CE

Distance between final.pdb #1.1/A ILE 538 CD1 and MET 534 CE: 4.894Å  

> distance #1.1/A:644@CD2 #1.1/A:534@CE

Distance between final.pdb #1.1/A LEU 644 CD2 and MET 534 CE: 6.570Å  

> save /Users/ksinha01/Kinases_local/FGFR1/pdbs/fgfr1_struc_nmr.cxs

> ~distance #1.1/A:538@CD1 #1.1/A:534@CE

> ~distance #1.1/A:537@CE #1.1/A:534@CE

> ~distance #1.1/A:644@CD2 #1.1/A:534@CE

> ~label

> label #1.1: 537

> distance #1.1/A:538@CD1 #1.1/A:537@CE

Distance between final.pdb #1.1/A ILE 538 CD1 and MET 537 CE: 5.283Å  

> ~distance #1.1/A:538@CD1 #1.1/A:537@CE

> ~label

> label #1.1: 535

> distance #1.1/A:544@CG1 #1.1/A:559@CG2

Distance between final.pdb #1.1/A ILE 544 CG1 and VAL 559 CG2: 16.069Å  

> ~distance #1.1/A:544@CG1 #1.1/A:559@CG2

> distance #1.1/A:559@CG2 #1.1/A:532@CE

Distance between final.pdb #1.1/A VAL 559 CG2 and MET 532 CE: 3.490Å  

> distance #1.1/A:552@CG2 #1.1/A:532@CE

Distance between final.pdb #1.1/A THR 552 CG2 and MET 532 CE: 4.591Å  

> distance #1.1/A:557@CD1 #1.1/A:532@CE

Distance between final.pdb #1.1/A LEU 557 CD1 and MET 532 CE: 3.647Å  

> distance #1.1/A:532@CE #1.1/A:465@CD1

Distance between final.pdb #1.1/A MET 532 CE and LEU 465 CD1: 3.298Å  

> distance #1.1/A:532@CE #1.1/A:528@CD2

Distance between final.pdb #1.1/A MET 532 CE and LEU 528 CD2: 5.929Å  

> distance #1.1/A:532@CE #1.1/A:529@CD1

Distance between final.pdb #1.1/A MET 532 CE and ILE 529 CD1: 5.029Å  

> distance #1.1/A:550@CB #1.1/A:532@CE

Distance between final.pdb #1.1/A ALA 550 CB and MET 532 CE: 5.210Å  

> ~distance #1.1/A:557@CD1 #1.1/A:532@CE

> ~distance #1.1/A:532@CE #1.1/A:465@CD1

> ~distance #1.1/A:532@CE #1.1/A:529@CD1

> ~distance #1.1/A:532@CE #1.1/A:528@CD2

> ~distance #1.1/A:559@CG2 #1.1/A:532@CE

> ~distance #1.1/A:550@CB #1.1/A:532@CE

> ~distance #1.1/A:552@CG2 #1.1/A:532@CE

> distance #1.1/A:547@CD2 #1.1/A:535@CE

Distance between final.pdb #1.1/A LEU 547 CD2 and MET 535 CE: 3.455Å  

> distance #1.1/A:561@CG1 #1.1/A:535@CE

Distance between final.pdb #1.1/A VAL 561 CG1 and MET 535 CE: 3.011Å  

> distance #1.1/A:545@CG2 #1.1/A:535@CE

Distance between final.pdb #1.1/A ILE 545 CG2 and MET 535 CE: 5.587Å  

> distance #1.1/A:535@CE #1.1/A:559@CG1

Distance between final.pdb #1.1/A MET 535 CE and VAL 559 CG1: 4.520Å  

> ~distance #1.1/A:545@CG2 #1.1/A:535@CE

> ~distance #1.1/A:547@CD2 #1.1/A:535@CE

> ~distance #1.1/A:535@CE #1.1/A:559@CG1

> ~distance #1.1/A:561@CG1 #1.1/A:535@CE

> distance #1.1/A:532@CE #1.1/A:535@CE

Distance between final.pdb #1.1/A MET 532 CE and MET 535 CE: 7.516Å  

> ~distance #1.1/A:532@CE #1.1/A:535@CE

> distance #1.1/A:550@CB #1.1/A:535@CE

Distance between final.pdb #1.1/A ALA 550 CB and MET 535 CE: 7.237Å  

> ~label

> label #1.1: 537

> distance #1.1/A:537@CE #1.1/A:538@CD1

Distance between final.pdb #1.1/A MET 537 CE and ILE 538 CD1: 5.283Å  

> distance #1.1/A:537@CE #1.1/A:534@CE

Distance between final.pdb #1.1/A MET 537 CE and MET 534 CE: 3.712Å  

> distance #1.1/A:614@CD2 #1.1/A:537@CE

Distance between final.pdb #1.1/A LEU 614 CD2 and MET 537 CE: 7.292Å  

> ~distance #1.1/A:614@CD2 #1.1/A:537@CE

> distance #1.1/A:644@CD2 #1.1/A:537@CE

Distance between final.pdb #1.1/A LEU 644 CD2 and MET 537 CE: 10.148Å  

> ~distance #1.1/A:644@CD2 #1.1/A:537@CE

> ~distance #1.1/A:537@CE #1.1/A:534@CE

> ~distance #1.1/A:537@CE #1.1/A:538@CD1

> ~label

> label #1.1: 719

> ~distance #1.1/A:550@CB #1.1/A:535@CE

> distance #1.1/A:688@CG1 #1.1/A:719@CE

Distance between final.pdb #1.1/A VAL 688 CG1 and MET 719 CE: 3.201Å  

> distance #1.1/A:719@CE #1.1/A:695@CG2

Distance between final.pdb #1.1/A MET 719 CE and THR 695 CG2: 6.669Å  

> distance #1.1/A:713@CD2 #1.1/A:719@CE

Distance between final.pdb #1.1/A LEU 713 CD2 and MET 719 CE: 8.712Å  

> ~distance #1.1/A:713@CD2 #1.1/A:719@CE

> ~label

> label #1.1: 515

> distance #1.1/A:493@CG2 #1.1/A:515@CE

Distance between final.pdb #1.1/A VAL 493 CG2 and MET 515 CE: 3.463Å  

> distance #1.1/A:515@CE #1.1/A:480@CD1

Distance between final.pdb #1.1/A MET 515 CE and LEU 480 CD1: 4.679Å  

> distance #1.1/A:513@CG1 #1.1/A:515@CE

Distance between final.pdb #1.1/A VAL 513 CG1 and MET 515 CE: 3.417Å  

> ~distance #1.1/A:672@CD2 #1.1/A:651@CD1

> ~distance #1.1/A:667@CE #1.1/A:672@CD2

> ~distance #1.1/A:493@CG2 #1.1/A:515@CE

> ~distance #1.1/A:515@CE #1.1/A:480@CD1

> ~distance #1.1/A:513@CG1 #1.1/A:515@CE

> ~label

> label #1.1: 667

> ~label

> label #1.1: 667,750

> ~distance #1.1/A:719@CE #1.1/A:695@CG2

> ~distance #1.1/A:688@CG1 #1.1/A:719@CE

> ~distance #1.1/A:678@CG2 #1.1/A:620@CD1

> ~label

> label #1.1: 667

> ~distance #1.1/A:664@CG1 #1.1/A:651@CD1

> distance #1.1/A:672@CD2 #1.1/A:648@CD1

Distance between final.pdb #1.1/A LEU 672 CD2 and ILE 648 CD1: 6.774Å  

> ~distance #1.1/A:672@CD2 #1.1/A:648@CD1

> distance #1.1/A:667@CE #1.1/A:648@CD1

Distance between final.pdb #1.1/A MET 667 CE and ILE 648 CD1: 3.862Å  

> ~distance #1.1/A:667@CE #1.1/A:648@CD1

> distance #1.1/A:664@CG1 #1.1/A:667@CE

Distance between final.pdb #1.1/A VAL 664 CG1 and MET 667 CE: 4.096Å  

> ~label

> label #1.1: 732

> distance #1.1/A:732@CE #1.1/A:750@CD2

Distance between final.pdb #1.1/A MET 732 CE and LEU 750 CD2: 4.665Å  

> distance #1.1/A:757@CD1 #1.1/A:732@CE

Distance between final.pdb #1.1/A ILE 757 CD1 and MET 732 CE: 3.634Å  

> distance #1.1/A:601@CG1 #1.1/A:732@CE

Distance between final.pdb #1.1/A VAL 601 CG1 and MET 732 CE: 7.431Å  

> distance #1.1/A:732@CE #1.1/A:690@CD2

Distance between final.pdb #1.1/A MET 732 CE and LEU 690 CD2: 5.039Å  

> distance #1.1/A:732@CE #1.1/A:754@CD2

Distance between final.pdb #1.1/A MET 732 CE and LEU 754 CD2: 4.067Å  

> distance #1.1/A:732@CE #1.1/A:729@CD2

Distance between final.pdb #1.1/A MET 732 CE and LEU 729 CD2: 4.576Å  

> distance #1.1/A:604@CB #1.1/A:732@CE

Distance between final.pdb #1.1/A ALA 604 CB and MET 732 CE: 6.940Å  

> ~distance #1.1/A:732@CE #1.1/A:750@CD2

> ~distance #1.1/A:757@CD1 #1.1/A:732@CE

> ~distance #1.1/A:604@CB #1.1/A:732@CE

> ~label

> label #1.1: 732,729

> ~distance #1.1/A:732@CE #1.1/A:729@CD2

> ~distance #1.1/A:601@CG1 #1.1/A:732@CE

> ~distance #1.1/A:732@CE #1.1/A:754@CD2

> ~distance #1.1/A:732@CE #1.1/A:690@CD2

> ~label

> label #1.1: 731

> ~label

> label #1.1: 733

> distance #1.1/A:757@CD1 #1.1/A:732@CE

Distance between final.pdb #1.1/A ILE 757 CD1 and MET 732 CE: 3.634Å  

> distance #1.1/A:732@CE #1.1/A:690@CD2

Distance between final.pdb #1.1/A MET 732 CE and LEU 690 CD2: 5.039Å  

> distance #1.1/A:729@CD2 #1.1/A:732@CE

Distance between final.pdb #1.1/A LEU 729 CD2 and MET 732 CE: 4.576Å  

> distance #1.1/A:732@CE #1.1/A:754@CD2

Distance between final.pdb #1.1/A MET 732 CE and LEU 754 CD2: 4.067Å  

> distance #1.1/A:604@CB #1.1/A:732@CE

Distance between final.pdb #1.1/A ALA 604 CB and MET 732 CE: 6.940Å  

> distance #1.1/A:750@CD2 #1.1/A:732@CE

Distance between final.pdb #1.1/A LEU 750 CD2 and MET 732 CE: 4.665Å  


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

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/ksinha01/Kinases_local/FGFR1/pdbs/fgfr1_struc_nmr.cxs

Log from Thu Mar 13 14:03:02 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/ksinha01/Kinases_local/FGFR1/pdbs/fgfr1_struc_nmr.cxs

Log from Thu Mar 13 10:39:34 2025

> alias dd distance delete

> alias rd ui mousemode right distance

> alias rs ui mousemode right select

> alias nmr1 hide #1.2-20 models

> alias slall label sel text
> "{0.label_one_letter_code}{0.number}{0.insertion_code}"

> alias lmearo label #1:thr,met,ala,leu,val,ile,phe,tyr text
> "{0.label_one_letter_code}{0.number}{0.insertion_code}"

> alias showbb show #1@N,C,CA,O,H; cartoon #1 suppress false; transparency #1
> 50 target c; hide #1:hoh

> alias hidebb hide #1@N,C,CA,O,H target a; transparency $1 0 target c

> alias sdist ui tool show Distances

> alias showmet show #1:ile,leu,val,met,ala,thr target a; hide H; color #1:ile
> paleturquoise target a; color #1:leu lightsalmon target a; color #1:val
> khaki target a; color #1:met thistle target a; color #1:ala yellowgreen
> target ab; color #1:thr aquamarine target a;color byhetero target a ; style
> #1 ball

> alias showmet2 show #2:ile,leu,val,met,ala,thr target a; hide H; color
> #2:ile paleturquoise target a; color #2:leu lightsalmon target a; color
> #2:val khaki target a; color #2:met thistle target a; color #2:ala
> yellowgreen target ab; color #2:thr aquamarine target a;color byhetero
> target a ; style #2 ball

> alias showmet3 show #3:ile,leu,val,met,ala,thr target a; hide H; color
> #3:ile paleturquoise target a; color #3:leu lightsalmon target a; color
> #3:val khaki target a; color #3:met thistle target a; color #3:ala
> yellowgreen target ab; color #3:thr aquamarine target a;color byhetero
> target a ; style #3 ball

> alias showaro show #1:phe,tyr,his,trp target ab; hide H; color #1:phe plum
> target a; color #1:tyr lightpink target a; color byhetero target a

> ui mousemode right distance

> alias fgfr1_brake show #1: 546,562,638

> alias fgfr2_brake show #1: 549,565,641

> alias fgfr3_brake show #1: 540,556,632

> alias fgfr4_brake show #1: 535,551,627

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/ksinha01/Kinases_local/FGFR1/FGFR1_struc_calc/fgfr1_040_4_brake_2_072_v13_082823/final.pdb

Chain information for final.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A | No description available  
  

> hide #1.2-20 cartoons

> hide #1.2-20

> showmet

Changed 98240 atom styles  

> hide #1.2-20

> set bgColor white

> label #1.1: 498

> distance #1.1/A:498@CD1 #1.1/A:508@CG1

Distance between final.pdb #1.1/A ILE 498 CD1 and VAL 508 CG1: 3.377Å  

> distance #1.1/A:498@CD1 #1.1/A:479@CG2

Distance between final.pdb #1.1/A ILE 498 CD1 and VAL 479 CG2: 5.271Å  

> distance #1.1/A:479@CG1 #1.1/A:498@CD1

Distance between final.pdb #1.1/A VAL 479 CG1 and ILE 498 CD1: 6.506Å  

> distance #1.1/A:498@CD1 #1.1/A:508@CG2

Distance between final.pdb #1.1/A ILE 498 CD1 and VAL 508 CG2: 3.465Å  

> label #1.1: 498,478

> label #1.1: 651

> distance #1.1/A:672@CD2 #1.1/A:651@CD1

Distance between final.pdb #1.1/A LEU 672 CD2 and ILE 651 CD1: 4.103Å  

> distance #1.1/A:651@CD1 #1.1/A:664@CG1

Distance between final.pdb #1.1/A ILE 651 CD1 and VAL 664 CG1: 5.547Å  

> distance #1.1/A:651@CD1 #1.1/A:667@CE

Distance between final.pdb #1.1/A ILE 651 CD1 and MET 667 CE: 5.814Å  

> ~distance #1.1/A:672@CD2 #1.1/A:651@CD1

> ~distance #1.1/A:651@CD1 #1.1/A:667@CE

> label #1.1: 651,493

> ~distance #1.1/A:651@CD1 #1.1/A:664@CG1

> distance #1.1/A:713@CD1 #1.1/A:651@CD1

Distance between final.pdb #1.1/A LEU 713 CD1 and ILE 651 CD1: 8.583Å  

> ~distance #1.1/A:713@CD1 #1.1/A:651@CD1

> label #1.1: 651,493,529

> distance #1.1/A:532@CE #1.1/A:529@CD1

Distance between final.pdb #1.1/A MET 532 CE and ILE 529 CD1: 5.029Å  

> distance #1.1/A:465@CD1 #1.1/A:529@CD1

Distance between final.pdb #1.1/A LEU 465 CD1 and ILE 529 CD1: 3.137Å  

> distance #1.1/A:529@CD1 #1.1/A:557@CD2

Distance between final.pdb #1.1/A ILE 529 CD1 and LEU 557 CD2: 3.651Å  

> distance #1.1/A:529@CD1 #1.1/A:528@CD2

Distance between final.pdb #1.1/A ILE 529 CD1 and LEU 528 CD2: 5.098Å  

> distance #1.1/A:529@CD1 #1.1/A:525@CD1

Distance between final.pdb #1.1/A ILE 529 CD1 and LEU 525 CD1: 3.179Å  

> distance #1.1/A:529@CD1 #1.1/A:516@CD1

Distance between final.pdb #1.1/A ILE 529 CD1 and LEU 516 CD1: 5.532Å  

> distance #1.1/A:552@CG2 #1.1/A:529@CD1

Distance between final.pdb #1.1/A THR 552 CG2 and ILE 529 CD1: 7.477Å  

> distance #1.1/A:532@CE #1.1/A:552@CG2

Distance between final.pdb #1.1/A MET 532 CE and THR 552 CG2: 4.591Å  

> ~distance #1.1/A:552@CG2 #1.1/A:529@CD1

> ~distance #1.1/A:532@CE #1.1/A:529@CD1

> ~distance #1.1/A:465@CD1 #1.1/A:529@CD1

> label #1.1: 651,493,631

> label #1.1: 651,493,631,479

> ~distance #1.1/A:529@CD1 #1.1/A:557@CD2

> ~distance #1.1/A:529@CD1 #1.1/A:516@CD1

> ~distance #1.1/A:529@CD1 #1.1/A:528@CD2

> ~distance #1.1/A:529@CD1 #1.1/A:525@CD1

> label #1.1: 651,493,631,479,693

> distance #1.1/A:693@CD1 #1.1/A:689@CD2

Distance between final.pdb #1.1/A ILE 693 CD1 and LEU 689 CD2: 4.294Å  

> distance #1.1/A:693@CD1 #1.1/A:690@CD2

Distance between final.pdb #1.1/A ILE 693 CD1 and LEU 690 CD2: 5.279Å  

> distance #1.1/A:693@CD1 #1.1/A:569@CD2

Distance between final.pdb #1.1/A ILE 693 CD1 and LEU 569 CD2: 4.038Å  

> distance #1.1/A:693@CD1 #1.1/A:595@CD1

Distance between final.pdb #1.1/A ILE 693 CD1 and LEU 595 CD1: 9.545Å  

> ~distance #1.1/A:693@CD1 #1.1/A:595@CD1

> distance #1.1/A:637@CE #1.1/A:693@CD1

Distance between final.pdb #1.1/A MET 637 CE and ILE 693 CD1: 5.340Å  

> distance #1.1/A:604@CB #1.1/A:693@CD1

Distance between final.pdb #1.1/A ALA 604 CB and ILE 693 CD1: 4.380Å  

> distance #1.1/A:693@CD1 #1.1/A:607@CG2

Distance between final.pdb #1.1/A ILE 693 CD1 and VAL 607 CG2: 4.552Å  

> ~distance #1.1/A:604@CB #1.1/A:693@CD1

> ~distance #1.1/A:693@CD1 #1.1/A:607@CG2

> ~distance #1.1/A:637@CE #1.1/A:693@CD1

> hide #1.2-20#!2 target m

> label #1.1: 521,657,658,493,624

> distance #1.1/A:639@CD1 #1.1/A:693@CD1

Distance between final.pdb #1.1/A ILE 639 CD1 and ILE 693 CD1: 9.000Å  

> distance #1.1/A:693@CD1 #1.1/A:639@CD1

Distance already exists; modify distance properties with 'distance style'  

> show #!2 models

> ~distance #1.1/A:639@CD1 #1.1/A:693@CD1

> ~label

> label #1.1: 706

> label #1.1: 706,651

> distance #1.1/A:706@CG1 #1.1/A:651@CD1

Distance between final.pdb #1.1/A VAL 706 CG1 and ILE 651 CD1: 7.471Å  

> distance #1.1/A:664@CG1 #1.1/A:651@CD1

Distance between final.pdb #1.1/A VAL 664 CG1 and ILE 651 CD1: 5.547Å  

> ~distance #1.1/A:706@CG1 #1.1/A:651@CD1

> distance #1.1/A:651@CD1 #1.1/A:709@CD2

Distance between final.pdb #1.1/A ILE 651 CD1 and LEU 709 CD2: 7.802Å  

> ~distance #1.1/A:651@CD1 #1.1/A:709@CD2

> distance #1.1/A:672@CD2 #1.1/A:651@CD1

Distance between final.pdb #1.1/A LEU 672 CD2 and ILE 651 CD1: 4.103Å  

> ~distance #1.1/A:672@CD2 #1.1/A:651@CD1

> distance #1.1/A:672@CD2 #1.1/A:651@CD1

Distance between final.pdb #1.1/A LEU 672 CD2 and ILE 651 CD1: 4.103Å  

> distance #1.1/A:667@CE #1.1/A:672@CD2

Distance between final.pdb #1.1/A MET 667 CE and LEU 672 CD2: 3.191Å  

> label #1.1: 706,651,657

> ~label

> label #1.1: 620

> distance #1.1/A:678@CG2 #1.1/A:620@CD1

Distance between final.pdb #1.1/A THR 678 CG2 and ILE 620 CD1: 5.652Å  

> label #1.1: 620,614

> label #1.1: 620,614,662

> ~label

> label #1.1: 560

> distance #1.1/A:560@CD1 #1.1/A:500@CD2

Distance between final.pdb #1.1/A ILE 560 CD1 and LEU 500 CD2: 5.520Å  

> distance #1.1/A:560@CD1 #1.1/A:478@CD2

Distance between final.pdb #1.1/A ILE 560 CD1 and LEU 478 CD2: 3.224Å  

> distance #1.1/A:560@CD1 #1.1/A:511@CG1

Distance between final.pdb #1.1/A ILE 560 CD1 and VAL 511 CG1: 5.731Å  

> distance #1.1/A:497@CB #1.1/A:560@CD1

Distance between final.pdb #1.1/A ALA 497 CB and ILE 560 CD1: 5.156Å  

> distance #1.1/A:560@CD1 #1.1/A:509@CG2

Distance between final.pdb #1.1/A ILE 560 CD1 and THR 509 CG2: 9.344Å  

> ~distance #1.1/A:560@CD1 #1.1/A:509@CG2

> distance #1.1/A:473@CD2 #1.1/A:560@CD1

Distance between final.pdb #1.1/A LEU 473 CD2 and ILE 560 CD1: 3.428Å  

> distance #1.1/A:548@CD1 #1.1/A:560@CD1

Distance between final.pdb #1.1/A LEU 548 CD1 and ILE 560 CD1: 7.353Å  

> ~distance #1.1/A:548@CD1 #1.1/A:560@CD1

> distance #1.1/A:560@CD1 #1.1/A:513@CG1

Distance between final.pdb #1.1/A ILE 560 CD1 and VAL 513 CG1: 5.569Å  

> label #1.1: 560,500,478,511,497,473,513,560

> label #1.1: 560,500,478,511,497,473,513,560,548

> distance #1.1/A:548@CD1 #1.1/A:560@CD1

Distance between final.pdb #1.1/A LEU 548 CD1 and ILE 560 CD1: 7.353Å  

> distance #1.1/A:548@CB #1.1/A:560@CD1

Distance between final.pdb #1.1/A LEU 548 CB and ILE 560 CD1: 5.998Å  

> ~distance #1.1/A:548@CD1 #1.1/A:560@CD1

> ~distance #1.1/A:498@CD1 #1.1/A:479@CG2

> label #1.1: 560,500,478,511,497,473,513,560,548,460

> ~distance #1.1/A:473@CD2 #1.1/A:560@CD1

> ~distance #1.1/A:560@CD1 #1.1/A:478@CD2

> ~label #1.1: 478,473

> ~distance #1.1/A:560@CD1 #1.1/A:513@CG1

> ~distance #1.1/A:560@CD1 #1.1/A:500@CD2

> ~distance #1.1/A:560@CD1 #1.1/A:511@CG1

> ~label

> label #1.1: 626

> ~distance #1.1/A:497@CB #1.1/A:560@CD1

> ~distance #1.1/A:548@CB #1.1/A:560@CD1

> ~distance #1.1/A:498@CD1 #1.1/A:508@CG1

> ~distance #1.1/A:479@CG1 #1.1/A:498@CD1

> ~distance #1.1/A:498@CD1 #1.1/A:508@CG2

> ~distance #1.1/A:693@CD1 #1.1/A:689@CD2

> ~distance #1.1/A:693@CD1 #1.1/A:569@CD2

> ~distance #1.1/A:693@CD1 #1.1/A:690@CD2

> distance #1.1/A:626@CB #1.1/A:693@CD1

Distance between final.pdb #1.1/A ALA 626 CB and ILE 693 CD1: 6.240Å  

> distance #1.1/A:626@CB #1.1/A:569@CD2

Distance between final.pdb #1.1/A ALA 626 CB and LEU 569 CD2: 3.655Å  

> ~distance #1.1/A:626@CB #1.1/A:693@CD1

> distance #1.1/A:626@CB #1.1/A:693@CD1

Distance between final.pdb #1.1/A ALA 626 CB and ILE 693 CD1: 6.240Å  

> distance #1.1/A:637@CE #1.1/A:626@CB

Distance between final.pdb #1.1/A MET 637 CE and ALA 626 CB: 6.865Å  

> ~distance #1.1/A:637@CE #1.1/A:626@CB

> distance #1.1/A:626@CB #1.1/A:689@CD1

Distance between final.pdb #1.1/A ALA 626 CB and LEU 689 CD1: 3.904Å  

> distance #1.1/A:607@CG2 #1.1/A:626@CB

Distance between final.pdb #1.1/A VAL 607 CG2 and ALA 626 CB: 7.870Å  

> ~distance #1.1/A:607@CG2 #1.1/A:626@CB

> distance #1.1/A:629@CG1 #1.1/A:626@CB

Distance between final.pdb #1.1/A VAL 629 CG1 and ALA 626 CB: 5.845Å  

> ~distance #1.1/A:629@CG1 #1.1/A:626@CB

> ~distance #1.1/A:626@CB #1.1/A:569@CD2

> ~distance #1.1/A:626@CB #1.1/A:693@CD1

> ~distance #1.1/A:626@CB #1.1/A:689@CD1

> show

> showmet

Changed 98240 atom styles  

> hide atoms

> showmet

Changed 98240 atom styles  

> show #1.1:653,654

> distance #1.1/A:626@CB #1.1/A:658@CG2

Distance between final.pdb #1.1/A ALA 626 CB and THR 658 CG2: 20.134Å  

> ~distance #1.1/A:626@CB #1.1/A:658@CG2

> label #1.1: 626,624

> distance #1.1/A:624@CD2 #1.1/A:626@CB

Distance between final.pdb #1.1/A LEU 624 CD2 and ALA 626 CB: 8.255Å  

> ~distance #1.1/A:624@CD2 #1.1/A:626@CB

> ~label

> label #1.1: 532

> distance #1.1/A:532@CE #1.1/A:465@CD1

Distance between final.pdb #1.1/A MET 532 CE and LEU 465 CD1: 3.298Å  

> distance #1.1/A:532@CE #1.1/A:529@CD1

Distance between final.pdb #1.1/A MET 532 CE and ILE 529 CD1: 5.029Å  

> distance #1.1/A:532@CE #1.1/A:557@CD1

Distance between final.pdb #1.1/A MET 532 CE and LEU 557 CD1: 3.647Å  

> distance #1.1/A:559@CG2 #1.1/A:532@CE

Distance between final.pdb #1.1/A VAL 559 CG2 and MET 532 CE: 3.490Å  

> distance #1.1/A:528@CD2 #1.1/A:532@CE

Distance between final.pdb #1.1/A LEU 528 CD2 and MET 532 CE: 5.929Å  

> ~distance #1.1/A:532@CE #1.1/A:529@CD1

> rota #1.1:535

rota is provided by the uninstalled bundle ISOLDE versions 1.7rc1 – 1.8  

> swappaa #1.1:535 MET

Unknown command: swappaa #1.1:535 MET  

> swapaa #1.1:535 MET

Using Dunbrack library  
final.pdb #1.1/A MET 535: phi -55.0, psi -33.6 trans  
Applying MET rotamer (chi angles: -178.6 179.7 71.4) to final.pdb #1.1/A MET
535  

> swapaa interactive #1.1:535 MET

final.pdb #1.1/A MET 535: phi -55.0, psi -33.6 trans  
Changed 135 bond radii  

> ~distance #1.1/A:532@CE #1.1/A:552@CG2

> ~distance #1.1/A:532@CE #1.1/A:465@CD1

> save /Users/ksinha01/Kinases_local/FGFR1/pdbs/fgfr1_struc_nmr.cxs

——— End of log from Thu Mar 13 10:39:34 2025 ———

opened ChimeraX session  

> ~distance #1.1/A:532@CE #1.1/A:557@CD1

> ~distance #1.1/A:559@CG2 #1.1/A:532@CE

> ~label

> label #1.1: 534

> ~distance #1.1/A:528@CD2 #1.1/A:532@CE

> distance #1.1/A:537@CE #1.1/A:534@CE

Distance between final.pdb #1.1/A MET 537 CE and MET 534 CE: 3.712Å  

> distance #1.1/A:538@CD1 #1.1/A:534@CE

Distance between final.pdb #1.1/A ILE 538 CD1 and MET 534 CE: 4.894Å  

> distance #1.1/A:644@CD2 #1.1/A:534@CE

Distance between final.pdb #1.1/A LEU 644 CD2 and MET 534 CE: 6.570Å  

> save /Users/ksinha01/Kinases_local/FGFR1/pdbs/fgfr1_struc_nmr.cxs

——— End of log from Thu Mar 13 14:03:02 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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: iMac
      Model Identifier: iMac20,1
      Processor Name: 10-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache (per Core): 256 KB
      L3 Cache: 20 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
      OS Loader Version: 580.140.1~8

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 22 hours, 39 minutes

Graphics/Displays:

    AMD Radeon Pro 5300:

      Chipset Model: AMD Radeon Pro 5300
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0047
      ROM Revision: 113-D3220I-231
      VBIOS Version: 113-D322A1XL-012
      Option ROM Version: 113-D322A1XL-012
      EFI Driver Version: 01.01.231
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG Ultra HD:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


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 (2)

comment:1 by Eric Pettersen, 7 months ago

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

comment:2 by Eric Pettersen, 7 months ago

Resolution: → duplicate
Status: assigned → closed
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