![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15901 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | 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-13.6.7-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.
My mac went to sleep and ChimeraX had crashed when I came back
Fatal Python error: Segmentation fault
Thread 0x000000031f5fa000 (most recent call first):
File "/Applications/apps_installed/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/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031e5f7000 (most recent call first):
File "/Applications/apps_installed/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/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031d5f4000 (most recent call first):
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/apps_installed/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/apps_installed/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/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031c5f1000 (most recent call first):
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031b5ee000 (most recent call first):
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000031a5eb000 (most recent call first):
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003195e8000 (most recent call first):
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003185e5000 (most recent call first):
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003175e2000 (most recent call first):
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003165df000 (most recent call first):
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003155dc000 (most recent call first):
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/apps_installed/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000202b3e280 (most recent call first):
File "/Applications/apps_installed/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/apps_installed/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/apps_installed/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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, chimerax.atomic._ribbons, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, psutil._psutil_osx, psutil._psutil_posix, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree (total: 66)
{"app_name":"ChimeraX","timestamp":"2024-09-06 22:12:37.00 -0700","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 13.6.7 (22G720)","roots_installed":0,"name":"ChimeraX","incident_id":"5CCEECE7-CFD7-4A01-89EC-7A64572B680A"}
{
"uptime" : 100000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 569,
"osVersion" : {
"train" : "macOS 13.6.7",
"build" : "22G720",
"releaseType" : "User"
},
"captureTime" : "2024-09-06 22:12:17.9428 -0700",
"incident" : "5CCEECE7-CFD7-4A01-89EC-7A64572B680A",
"pid" : 490,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-04 11:26:52.1072 -0700",
"procStartAbsTime" : 833525123,
"procExitAbsTime" : 2596098865732,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5EAECDE7-CBF1-5097-855E-E117783BF094","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C819F76F-3813-8349-EFEF-695E46CF7FE0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 1,
"sleepWakeUUID" : "F8BA6B3D-A08D-46EF-A3A5-9EF2849FD59B",
"sip" : "enabled",
"vmRegionInfo" : "0x10fa9754218 is not in any region. Bytes after previous region: 685742834201 Bytes before following region: 104386337095144\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000810fa9754218","rawCodes":[1,141904267526680],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000810fa9754218 -> 0x0000010fa9754218 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":490},
"vmregioninfo" : "0x10fa9754218 is not in any region. Bytes after previous region: 685742834201 Bytes before following region: 104386337095144\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"name" : "QtOpenGLWidgets.abi3.so"
},
{
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"size" : 49152,
"uuid" : "c84a9a90-56dd-385a-aad3-a15d44bc216b",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
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"uuid" : "08a0cdf4-85d3-328a-98ac-8a7ec48356eb",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5931986944,
"size" : 147456,
"uuid" : "a66bb1e2-ecf4-3220-9c8e-a465d9305940",
"path" : "\/Applications\/apps_installed\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
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"arch" : "x86_64",
"base" : 140703536922624,
"size" : 237568,
"uuid" : "e82b6d50-ac03-370d-a74d-eb1a2725b6c5",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703537160192,
"size" : 49152,
"uuid" : "60b15e1f-39ea-33a1-8616-3af57dc1094a",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703535771648,
"size" : 557048,
"uuid" : "a720129c-c1cf-3e62-9d76-aa6fa0d31333",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
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"arch" : "x86_64",
"base" : 140703537356800,
"size" : 40944,
"uuid" : "982c4eec-b380-3c37-ab95-14150e14dd61",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703588143104,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16814080,
"uuid" : "0de06622-e926-3354-8b51-b64f04f21173",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.77.138"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703616712704,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4141050,
"uuid" : "b6fc2ba6-9ebb-31df-8dd2-e458b4e0c9a5",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
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"size" : 294900,
"uuid" : "9e8b726d-ca70-32d6-8987-0fa21014ec5b",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703537573888,
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"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4829184,
"uuid" : "662e85ab-b3a3-3663-b31d-3424dc50d464",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1979.104"
},
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"source" : "P",
"arch" : "x86_64",
"base" : 140703704928256,
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"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3112954,
"uuid" : "1afba695-4d4c-3b3e-9911-92f50c585ba4",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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"arch" : "x86_64",
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"size" : 507896,
"uuid" : "c39b7907-eabb-3019-aab0-f6aea01d5c1a",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=6.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.6G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 8704K 10 \nCG image 360K 49 \nColorSync 264K 30 \nCoreAnimation 912K 93 \nCoreGraphics 8K 2 \nCoreServices 624K 2 \nCoreUI image data 2444K 20 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 4.9G 1672 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 368.0M 5 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 24K 6 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1736K 431 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 1228K 118 \nRosetta Thread Context 1180K 118 \nSTACK GUARD 28K 7 \nStack 342.7M 59 \nStack Guard 56.2M 52 \nVM_ALLOCATE 266.0M 560 \nVM_ALLOCATE (reserved) 128.1M 13 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 46.5M 882 \n__DATA_CONST 55.8M 516 \n__DATA_DIRTY 2067K 267 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 204.0M 172 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2011K 2 \n__TEXT 1.0G 886 \ndyld private memory 292K 4 \nmapped file 4.9G 1835 \nshared memory 3060K 31 \nunshared pmap 15.5M 10 \n=========== ======= ======= \nTOTAL 13.0G 7883 \nTOTAL, minus reserved VM space 12.1G 7883 \n",
"legacyInfo" : {
"threadTriggered" : {
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"queue" : "com.apple.main-thread"
}
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"logWritingSignature" : "4c1f857c2a42eb70a97b31a2303731504cd8f5dc",
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"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> alias nice cartoon suppressBackboneDisplay false; cartoon style width 1;
> size stickRadius 0.12
> lighting soft
> nice
Changed 0 bond radii
> alias voltr5 vol transparency 0.5
> alias voltroff vol transparency 0
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> alias cartoonDefaults cartoon style protein modeh default
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
3418 messages similar to the above omitted
Chain information for zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb #1
---
Chain | Description
A B | No description available
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
3270 messages similar to the above omitted
Chain information for zfO1_NC2_10mM_bestModel_apo.pdb #2
---
Chain | Description
A B | No description available
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/SWISSMODEL_results/mO1_dimer_on_zfO1_C2.2_apo_model_01.pdb"
mO1_dimer_on_zfO1_C2.2_apo_model_01.pdb title:
SWISS-MODEL SERVER (https://swissmodel.expasy.org) mO1_on_zfO1_C2.2_apo [more
info...]
Chain information for mO1_dimer_on_zfO1_C2.2_apo_model_01.pdb #3
---
Chain | Description
A B | No description available
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF2_dockings/hOtop1_AF/hO1_aligned.pdb"
hO1_aligned.pdb title:
Alphafold V2.0 prediction for proton channel OTOP1 (Q7RTM1) [more info...]
Chain information for hO1_aligned.pdb #4
---
Chain | Description | UniProt
A | proton channel OTOP1 | OTOP1_HUMAN 1-612
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF2_dockings/mOtop1_AF/mO1_aligned.pdb"
mO1_aligned.pdb title:
Alphafold V2.0 prediction for proton channel OTOP1 (Q80VM9) [more info...]
Chain information for mO1_aligned.pdb #5
---
Chain | Description | UniProt
A | proton channel OTOP1 | OTOP1_MOUSE 1-600
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_mo1_monomer/fold_mo1_monomer_model_4.cif"
Chain information for fold_mo1_monomer_model_4.cif #6
---
Chain | Description
A | .
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_mo1_monomer/fold_mo1_monomer_model_3.cif"
Chain information for fold_mo1_monomer_model_3.cif #7
---
Chain | Description
A | .
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_mo1_monomer/fold_mo1_monomer_model_2.cif"
Chain information for fold_mo1_monomer_model_2.cif #8
---
Chain | Description
A | .
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_mo1_monomer/fold_mo1_monomer_model_1.cif"
Chain information for fold_mo1_monomer_model_1.cif #9
---
Chain | Description
A | .
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_mo1_monomer/fold_mo1_monomer_model_0.cif"
Chain information for fold_mo1_monomer_model_0.cif #10
---
Chain | Description
A | .
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_ho1_monomer/fold_ho1_monomer_model_4.cif"
Chain information for fold_ho1_monomer_model_4.cif #11
---
Chain | Description
A | .
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_ho1_monomer/fold_ho1_monomer_model_3.cif"
Chain information for fold_ho1_monomer_model_3.cif #12
---
Chain | Description
A | .
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_ho1_monomer/fold_ho1_monomer_model_2.cif"
Chain information for fold_ho1_monomer_model_2.cif #13
---
Chain | Description
A | .
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_ho1_monomer/fold_ho1_monomer_model_1.cif"
Chain information for fold_ho1_monomer_model_1.cif #14
---
Chain | Description
A | .
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_AF3_dockings/fold_ho1_monomer/fold_ho1_monomer_model_0.cif"
Chain information for fold_ho1_monomer_model_0.cif #15
---
Chain | Description
A | .
> hide models
> show #!1 models
> show #4 models
> hide #!1 models
> lighting soft
> show
> show #!1 models
> mmaker #4,5 to #1/A
Parameters
---
Chain pairing | bb
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 zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with hO1_aligned.pdb, chain A (#4), sequence alignment score = 1156.9
RMSD between 181 pruned atom pairs is 1.108 angstroms; (across all 389 pairs:
5.671)
Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with mO1_aligned.pdb, chain A (#5), sequence alignment score = 1145.5
RMSD between 183 pruned atom pairs is 1.079 angstroms; (across all 389 pairs:
4.816)
> hide #!1 models
> show #!1 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #4 models
> hide #5 models
> show #10 models
> mmaker #6-15to #1/A
> matchmaker #6-15to #1/A
Missing or invalid "matchAtoms" argument: only initial part "#6-15" of atom
specifier valid
> mmaker #6-15 to #1/A
Parameters
---
Chain pairing | bb
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 zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with fold_mo1_monomer_model_4.cif, chain A (#6), sequence alignment score =
1148.5
RMSD between 270 pruned atom pairs is 1.222 angstroms; (across all 389 pairs:
4.343)
Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with fold_mo1_monomer_model_3.cif, chain A (#7), sequence alignment score =
1146.1
RMSD between 230 pruned atom pairs is 1.153 angstroms; (across all 389 pairs:
4.456)
Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with fold_mo1_monomer_model_2.cif, chain A (#8), sequence alignment score =
1142.5
RMSD between 283 pruned atom pairs is 1.240 angstroms; (across all 389 pairs:
4.179)
Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with fold_mo1_monomer_model_1.cif, chain A (#9), sequence alignment score =
1142.5
RMSD between 241 pruned atom pairs is 1.153 angstroms; (across all 389 pairs:
4.308)
Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with fold_mo1_monomer_model_0.cif, chain A (#10), sequence alignment score =
1135.3
RMSD between 223 pruned atom pairs is 1.079 angstroms; (across all 389 pairs:
4.409)
Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with fold_ho1_monomer_model_4.cif, chain A (#11), sequence alignment score =
1165.7
RMSD between 310 pruned atom pairs is 1.150 angstroms; (across all 389 pairs:
4.983)
Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with fold_ho1_monomer_model_3.cif, chain A (#12), sequence alignment score =
1169.3
RMSD between 304 pruned atom pairs is 1.185 angstroms; (across all 389 pairs:
5.005)
Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with fold_ho1_monomer_model_2.cif, chain A (#13), sequence alignment score =
1165.1
RMSD between 240 pruned atom pairs is 1.204 angstroms; (across all 389 pairs:
5.086)
Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with fold_ho1_monomer_model_1.cif, chain A (#14), sequence alignment score =
1168.7
RMSD between 232 pruned atom pairs is 1.180 angstroms; (across all 389 pairs:
5.162)
Matchmaker zfO1_NC2_10mM_bestModel_w8copiesOfNC2_C2dimer.pdb, chain A (#1)
with fold_ho1_monomer_model_0.cif, chain A (#15), sequence alignment score =
1168.7
RMSD between 211 pruned atom pairs is 1.217 angstroms; (across all 389 pairs:
5.209)
> lighting simple
> show #9 models
> show #8 models
> show #7 models
> show #6 models
> show #11 models
> show #12 models
> show #13 models
> show #14 models
> show #15 models
> hide #!1 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> show #15 models
> hide #11 models
> hide #12 models
> hide #13 models
> hide #14 models
> show #4 models
> hide #15 models
> show #15 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #4 models
> hide #15 models
> show #10 models
> hide #!1 models
> show #9 models
> show #8 models
> show #7 models
> show #6 models
> show #!1 models
> hide #!1 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> hide #6 models
> hide #7 models
> hide #9 models
> hide #8 models
> show #5 models
> hide #5 models
> show #5 models
> show #!1 models
> hide #10 models
> show #10 models
> show #15 models
> hide #15 models
> show #15 models
> hide #15 models
> hide #5 models
> hide #10 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #!1 models
> view 1/A:267
Expected an objects specifier or a view name or a keyword
> view #1/A:267
> ui tool show "Add Hydrogens"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> addh #!2 hbond false
Summary of feedback from adding hydrogens to zfO1_NC2_10mM_bestModel_apo.pdb
#2
---
notes | No usable SEQRES records for zfO1_NC2_10mM_bestModel_apo.pdb (#2) chain A; guessing termini instead
No usable SEQRES records for zfO1_NC2_10mM_bestModel_apo.pdb (#2) chain B;
guessing termini instead
Chain-initial residues that are actual N termini:
zfO1_NC2_10mM_bestModel_apo.pdb #2/A TYR 47, zfO1_NC2_10mM_bestModel_apo.pdb
#2/B TYR 47
Chain-initial residues that are not actual N termini:
zfO1_NC2_10mM_bestModel_apo.pdb #2/A ALA 124, zfO1_NC2_10mM_bestModel_apo.pdb
#2/A ALA 158, zfO1_NC2_10mM_bestModel_apo.pdb #2/A LYS 187,
zfO1_NC2_10mM_bestModel_apo.pdb #2/A SER 252, zfO1_NC2_10mM_bestModel_apo.pdb
#2/A LEU 305, zfO1_NC2_10mM_bestModel_apo.pdb #2/A MET 334,
zfO1_NC2_10mM_bestModel_apo.pdb #2/A ASN 376, zfO1_NC2_10mM_bestModel_apo.pdb
#2/A GLY 511, zfO1_NC2_10mM_bestModel_apo.pdb #2/B ALA 124,
zfO1_NC2_10mM_bestModel_apo.pdb #2/B ALA 158, zfO1_NC2_10mM_bestModel_apo.pdb
#2/B LYS 187, zfO1_NC2_10mM_bestModel_apo.pdb #2/B SER 252,
zfO1_NC2_10mM_bestModel_apo.pdb #2/B LEU 305, zfO1_NC2_10mM_bestModel_apo.pdb
#2/B MET 334, zfO1_NC2_10mM_bestModel_apo.pdb #2/B ASN 376,
zfO1_NC2_10mM_bestModel_apo.pdb #2/B GLY 511
Chain-final residues that are actual C termini:
zfO1_NC2_10mM_bestModel_apo.pdb #2/A LYS 585, zfO1_NC2_10mM_bestModel_apo.pdb
#2/B LYS 585
Chain-final residues that are not actual C termini:
zfO1_NC2_10mM_bestModel_apo.pdb #2/A ARG 110, zfO1_NC2_10mM_bestModel_apo.pdb
#2/A HIS 153, zfO1_NC2_10mM_bestModel_apo.pdb #2/A ASP 184,
zfO1_NC2_10mM_bestModel_apo.pdb #2/A THR 216, zfO1_NC2_10mM_bestModel_apo.pdb
#2/A ARG 285, zfO1_NC2_10mM_bestModel_apo.pdb #2/A HIS 327,
zfO1_NC2_10mM_bestModel_apo.pdb #2/A THR 373, zfO1_NC2_10mM_bestModel_apo.pdb
#2/A ARG 443, zfO1_NC2_10mM_bestModel_apo.pdb #2/B ARG 110,
zfO1_NC2_10mM_bestModel_apo.pdb #2/B HIS 153, zfO1_NC2_10mM_bestModel_apo.pdb
#2/B ASP 184, zfO1_NC2_10mM_bestModel_apo.pdb #2/B THR 216,
zfO1_NC2_10mM_bestModel_apo.pdb #2/B ARG 285, zfO1_NC2_10mM_bestModel_apo.pdb
#2/B HIS 327, zfO1_NC2_10mM_bestModel_apo.pdb #2/B THR 373,
zfO1_NC2_10mM_bestModel_apo.pdb #2/B ARG 443
Adding 'H' to zfO1_NC2_10mM_bestModel_apo.pdb #2/A ALA 124
Adding 'H' to zfO1_NC2_10mM_bestModel_apo.pdb #2/A ALA 158
Adding 'H' to zfO1_NC2_10mM_bestModel_apo.pdb #2/A LYS 187
Adding 'H' to zfO1_NC2_10mM_bestModel_apo.pdb #2/A SER 252
Adding 'H' to zfO1_NC2_10mM_bestModel_apo.pdb #2/A LEU 305
11 messages similar to the above omitted
6828 hydrogens added
> hide #!2 models
> show #!2 models
> ui tool show "Add Charges"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Add Hydrogens"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb"
Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16
---
Chain | Description
A | No description available
> hide #!2 models
> show
> ui tool show "Add Hydrogens"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> addh #!16
Summary of feedback from adding hydrogens to
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16
---
notes | No usable SEQRES records for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb (#16) chain A; guessing termini instead
Chain-initial residues that are actual N termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A TYR 47
Chain-initial residues that are not actual N termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ALA 124,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ALA 158,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A LYS 187,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A SER 252,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A LEU 305,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A MET 334,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ASN 376,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A GLY 511
Chain-final residues that are actual C termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A LYS 585
Chain-final residues that are not actual C termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ARG 110,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A HIS 153,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ASP 184,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A THR 216,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ARG 285,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A HIS 327,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A THR 373,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ARG 443
440 hydrogen bonds
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ALA 124
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A ALA 158
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A LYS 187
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A SER 252
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #16/A LEU 305
3 messages similar to the above omitted
3171 hydrogens added
> pwd
Current working directory is: /Users/bburendei/Desktop
> cd "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking"
Current working directory is: /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking
> save zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot_addH.pdb models #16
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE_E267protTest.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE_E267protTest.pdb
---
warnings | Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
3154 messages similar to the above omitted
Chain information for
zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE_E267protTest.pdb #17
---
Chain | Description
A | No description available
> hide #!16 models
> show
> show #!16 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot_REDUCE.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot_REDUCE.pdb
---
warnings | Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
3147 messages similar to the above omitted
Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot_REDUCE.pdb
#18
---
Chain | Description
A | No description available
> hide #!17 models
> hide #!16 models
> hide #!18 models
> show #!18 models
> showq
Unknown command: showq
> show
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> addH
Unknown command: addH
> AddH
Unknown command: AddH
> hide #!18 models
> show #!16 models
> show #!17 models
> hide #!16 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb"
Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19
---
Chain | Description
A | No description available
> show
> addh #19
Summary of feedback from adding hydrogens to
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19
---
notes | No usable SEQRES records for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb (#19) chain A; guessing termini instead
Chain-initial residues that are actual N termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A TYR 47
Chain-initial residues that are not actual N termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ALA 124,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ALA 158,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A LYS 187,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A SER 252,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A LEU 305,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A MET 334,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ASN 376,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A GLY 511
Chain-final residues that are actual C termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A LYS 585
Chain-final residues that are not actual C termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ARG 110,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A HIS 153,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ASP 184,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A THR 216,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ARG 285,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A HIS 327,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A THR 373,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ARG 443
440 hydrogen bonds
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ALA 124
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A ALA 158
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A LYS 187
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A SER 252
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #19/A LEU 305
3 messages similar to the above omitted
3171 hydrogens added
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb"
Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20
---
Chain | Description
A | No description available
> hide #!19 models
> hide #!20 models
> show #!20 models
> show
> addh #20/A:267
Summary of feedback from adding hydrogens to
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20
---
notes | No usable SEQRES records for zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb (#20) chain A; guessing termini instead
Chain-initial residues that are actual N termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A TYR 47
Chain-initial residues that are not actual N termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ALA 124,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ALA 158,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A LYS 187,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A SER 252,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A LEU 305,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A MET 334,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ASN 376,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A GLY 511
Chain-final residues that are actual C termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A LYS 585
Chain-final residues that are not actual C termini:
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ARG 110,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A HIS 153,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ASP 184,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A THR 216,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ARG 285,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A HIS 327,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A THR 373,
zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ARG 443
440 hydrogen bonds
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ALA 124
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A ALA 158
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A LYS 187
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A SER 252
Adding 'H' to zfO1_NC2_10mM_bestModel_apo_chAclean_E267prot.pdb #20/A LEU 305
3 messages similar to the above omitted
3171 hydrogens added
> settatr
Unknown command: settatr
> setatr
Unknown command: setatr
> setattr
Missing or invalid "target" argument: Expected a text string
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!20 models
> show #!20 models
> setattr #20/A:267 residue name GLU
Assigning name attribute to 1 item
> setattr #20/A:267 residue name GLH
Assigning name attribute to 1 item
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdb
---
warnings | Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
Duplicate atom serial number found: 0
3154 messages similar to the above omitted
Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdb
#21
---
Chain | Description
A | No description available
> hide #!20 models
> hide #!21 models
> show #!21 models
> show
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdbqt"
Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdb
#22
---
Chain | Description
A | No description available
Opened zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdbqt containing 1
structures (3755 atoms, 3831 bonds)
> hide #!21 models
> show
> clip off
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE.pdbqt"
Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE.pdb #23
---
Chain | Description
A | No description available
Opened zfO1_NC2_10mM_bestModel_apo_chAclean_REDUCE.pdbqt containing 1
structures (3754 atoms, 3830 bonds)
> hide #!22 models
> show
> hide #!23 models
> show #!22 models
> show #!23 models
> hide #!23 models
> hide #!22 models
> show #!16 models
> hide #!16 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo_chAclean.pdb"
Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean.pdb #24
---
Chain | Description
A | No description available
> show
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> hide #!22 models
> show #!22 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240328_zfO1_newStructures_smols_docking/zfO1_NC2_10mM_F570outerSite_TRP126FLEX_reDocks/zfO1_F570_outer_site_bare_BOX.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240328_zfO1_newStructures_smols_docking/zfO1_NC2_10mM_F570outerSite_TRP126FLEX_reDocks/zfO1_F570_outer_site_bare_BOX.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK This is the box from the file : zfO1_F570_outer_site_bare.gpf
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240328_zfO1_newStructures_smols_docking/cryosparc_P120_J3424_008_volume_map_sharp.mrc"
Opened cryosparc_P120_J3424_008_volume_map_sharp.mrc as #26, grid size
200,200,200, pixel 1.07, shown at level 0.371, step 1, values float32
> volume #26 level 0.939
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/control_zfO1_C2.2_chA_reDocking/GLH267_only_vina/CB68710218_C2.36_to_zfO1_C2.2_GLH267_out.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/control_zfO1_C2.2_chA_reDocking/GLH267_only_vina/CB68710218_C2.36_to_zfO1_C2.2_GLH267_out.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -9.037 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -10.132
Ignored bad PDB record found on line 4
REMARK INTER: -10.011
Ignored bad PDB record found on line 5
REMARK INTRA: -0.121
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.303
166 messages similar to the above omitted
Opened CB68710218_C2.36_to_zfO1_C2.2_GLH267_out.pdbqt containing 9 structures
(198 atoms, 225 bonds)
> viewdockx #27.1-9
> voltr5
> view #27
> hide #27.2 models
> hide #27.3 models
> hide #27.4 models
> hide #27.1,5-9 models
> show #27.6 models
> show #27.5 models
> hide #27.5-6 models
> show #27.6 models
> show #27.5 models
> hide #27.5 models
> hide #27.6 models
> show #27.6 models
> hide #27.6 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> hide #27.1 models
> show #27.1 models
> ui tool show "Side View"
> hide #27.1 models
> show #27.2 models
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> show #27.3 models
> hide #27.3 models
> show #27.2 models
> hide #27.2 models
> show #27.3 models
> hide #27.3 models
> show #27.4 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240328_zfO1_newStructures_smols_docking/cryosparc_P120_J2922_005_volume_map_sharp.mrc"
Opened cryosparc_P120_J2922_005_volume_map_sharp.mrc as #28, grid size
200,200,200, pixel 1.04, shown at level 0.0781, step 1, values float32
> view
> volume #28 level 0.2402
> fitmap #28 inMap #26
Fit map cryosparc_P120_J2922_005_volume_map_sharp.mrc in map
cryosparc_P120_J3424_008_volume_map_sharp.mrc using 22339 points
correlation = 0.2658, correlation about mean = 0.09642, overlap = 4230
steps = 104, shift = 0.849, angle = 9.49 degrees
Position of cryosparc_P120_J2922_005_volume_map_sharp.mrc (#28) relative to
cryosparc_P120_J3424_008_volume_map_sharp.mrc (#26) coordinates:
Matrix rotation and translation
0.98764353 0.07825688 -0.13577969 7.55735375
-0.07110994 0.99585461 0.05671837 1.17503716
0.13965543 -0.04636224 0.98911420 -8.98840843
Axis -0.31250818 -0.83503318 -0.45283354
Axis point 66.00373887 0.00000000 51.32634286
Rotation angle (degrees) 9.49285738
Shift along axis 0.72732290
> ui mousemode right translate
> select add #28
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.98764,0.078257,-0.13578,11.111,-0.07111,0.99585,0.056718,3.802,0.13966,-0.046362,0.98911,-8.916
> view matrix models
> #28,0.98764,0.078257,-0.13578,11.45,-0.07111,0.99585,0.056718,6.0462,0.13966,-0.046362,0.98911,-9.5918
> fitmap #28 inMap #26
Fit map cryosparc_P120_J2922_005_volume_map_sharp.mrc in map
cryosparc_P120_J3424_008_volume_map_sharp.mrc using 22339 points
correlation = 0.8531, correlation about mean = 0.5538, overlap = 1.979e+04
steps = 96, shift = 4.04, angle = 9.61 degrees
Position of cryosparc_P120_J2922_005_volume_map_sharp.mrc (#28) relative to
cryosparc_P120_J3424_008_volume_map_sharp.mrc (#26) coordinates:
Matrix rotation and translation
0.99999108 -0.00422418 0.00001892 2.66215676
0.00422418 0.99999108 -0.00000358 1.78465294
-0.00001890 0.00000366 1.00000000 2.04039659
Axis 0.00085787 0.00447662 0.99998961
Axis point -418.97955466 630.68673302 0.00000000
Rotation angle (degrees) 0.24203105
Shift along axis 2.05064839
> select subtract #28
Nothing selected
> ui mousemode right "next docked"
> viewdockx down
> hide #27.4 models
> show #27.5 models
> viewdockx down
> hide #27.5 models
> show #27.6 models
> viewdockx down
> hide #27.6 models
> show #27.7 models
> viewdockx down
> hide #27.7 models
> show #27.8 models
> viewdockx down
> hide #27.8 models
> show #27.9 models
> viewdockx down
> viewdockx up
> hide #27.9 models
> show #27.8 models
> viewdockx up
> hide #27.8 models
> show #27.7 models
> viewdockx up
> hide #27.7 models
> show #27.6 models
> viewdockx up
> hide #27.6 models
> show #27.5 models
> viewdockx down
> hide #27.5 models
> show #27.6 models
> viewdockx down
> hide #27.6 models
> show #27.7 models
> viewdockx down
> hide #27.7 models
> show #27.8 models
> viewdockx down
> hide #27.8 models
> show #27.9 models
> viewdockx down
> viewdockx up
> hide #27.9 models
> show #27.8 models
> viewdockx up
> hide #27.8 models
> show #27.7 models
> viewdockx up
> hide #27.7 models
> show #27.6 models
> viewdockx up
> hide #27.6 models
> show #27.5 models
> viewdockx down
> hide #27.5 models
> show #27.6 models
> viewdockx down
> hide #27.6 models
> show #27.7 models
> viewdockx down
> hide #27.7 models
> show #27.8 models
> viewdockx down
> hide #27.8 models
> show #27.9 models
> viewdockx up
> hide #27.9 models
> show #27.8 models
> viewdockx down
> hide #27.8 models
> show #27.9 models
> viewdockx down
> viewdockx up
> hide #27.9 models
> show #27.8 models
> viewdockx up
> hide #27.8 models
> show #27.7 models
> viewdockx up
> hide #27.7 models
> show #27.6 models
> viewdockx up
> hide #27.6 models
> show #27.5 models
> viewdockx up
> hide #27.5 models
> show #27.4 models
> viewdockx up
> hide #27.4 models
> show #27.3 models
> viewdockx up
> hide #27.3 models
> show #27.2 models
> viewdockx up
> hide #27.2 models
> show #27.1 models
> viewdockx up
> voltr5
> view #27.1
> viewdockx down
> hide #27.1 models
> show #27.2 models
> viewdockx down
> hide #27.2 models
> show #27.3 models
> viewdockx down
> hide #27.3 models
> show #27.4 models
> viewdockx down
> hide #27.4 models
> show #27.5 models
> viewdockx down
> hide #27.5 models
> show #27.6 models
> viewdockx up
> hide #27.6 models
> show #27.5 models
> viewdockx down
> hide #27.5 models
> show #27.6 models
> viewdockx down
> hide #27.6 models
> show #27.7 models
> viewdockx up
> hide #27.7 models
> show #27.6 models
> viewdockx down
> hide #27.6 models
> show #27.7 models
> viewdockx up
> hide #27.7 models
> show #27.6 models
> viewdockx up
> hide #27.6 models
> show #27.5 models
> viewdockx up
> hide #27.5 models
> show #27.4 models
> viewdockx down
> hide #27.4 models
> show #27.5 models
> viewdockx up
> hide #27.5 models
> show #27.4 models
> viewdockx up
> hide #27.4 models
> show #27.3 models
> viewdockx up
> hide #27.3 models
> show #27.2 models
> viewdockx up
> hide #27.2 models
> show #27.1 models
> viewdockx up
> volume #28 level 0.3802
> volume #28 level 0.2549
> viewdockx up
> viewdockx down
> hide #27.1 models
> show #27.2 models
> viewdockx down
> hide #27.2 models
> show #27.3 models
> viewdockx down
> hide #27.3 models
> show #27.4 models
> viewdockx down
> hide #27.4 models
> show #27.5 models
> viewdockx down
> hide #27.5 models
> show #27.6 models
> viewdockx down
> hide #27.6 models
> show #27.7 models
> viewdockx down
> hide #27.7 models
> show #27.8 models
> viewdockx up
> hide #27.8 models
> show #27.7 models
> viewdockx up
> hide #27.7 models
> show #27.6 models
> viewdockx up
> hide #27.6 models
> show #27.5 models
> viewdockx up
> hide #27.5 models
> show #27.4 models
> viewdockx up
> hide #27.4 models
> show #27.3 models
> viewdockx up
> hide #27.3 models
> show #27.2 models
> viewdockx up
> hide #27.2 models
> show #27.1 models
> viewdockx up
> show #!28 models
> viewdockx down
> hide #27.1 models
> show #27.2 models
> viewdockx up
> hide #27.2 models
> show #27.1 models
> viewdockx up
> viewdockx down
> hide #27.1 models
> show #27.2 models
> viewdockx down
> hide #27.2 models
> show #27.3 models
> viewdockx down
> hide #27.3 models
> show #27.4 models
> viewdockx down
> hide #27.4 models
> show #27.5 models
> viewdockx down
> hide #27.5 models
> show #27.6 models
> viewdockx down
> hide #27.6 models
> show #27.7 models
> viewdockx down
> hide #27.7 models
> show #27.8 models
> viewdockx down
> hide #27.8 models
> show #27.9 models
> viewdockx down
> viewdockx up
> hide #27.9 models
> show #27.8 models
> viewdockx up
> hide #27.8 models
> show #27.7 models
> viewdockx up
> hide #27.7 models
> show #27.6 models
> hide #27.6 models
> show #27.9 models
> hide #27.9 models
> show #27.8 models
> hide #27.8 models
> show #27.7 models
> show #27.6 models
> show #27.5 models
> hide #27.5 models
> hide #27.6 models
> hide #27.7 models
> show #27.7 models
> show #27.5 models
> hide #27.7 models
> hide #27.5 models
> show #27.4 models
> hide #27.4 models
> show #27.3 models
> show #27.1 models
> hide #27.3 models
> hide #27.1 models
> show #27.2 models
> hide #27.2 models
> show #27.1 models
> hide #27.1 models
> show #27.2 models
> hide #27.2 models
> show #27.1 models
> hide #27.1 models
> show #27.2 models
> hide #27.2 models
> show #27.1 models
> hide #27.1 models
> show #27.2 models
> hide #27.2 models
> show #27.3 models
> hide #27.3 models
> show #27.1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #27
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer.pdb"
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> hide #27 models
> show #27 models
> color #29 #d58258ff
> color #29 byhetero
> rmsd
Missing or invalid "atoms" argument: empty atom specifier
> rmsd #27 #29
Missing required "to" argument
> rmsd #27 tot #29
Expected a keyword
> rmsd #27 to #29
RMSD between 22 atom pairs is 3.588
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #29 models
> show #29 models
> rmsd #29 to #1/A:609
Number of atoms from first atom spec (22) differs from number in second (37)
> rmsd #29 to #1/A:609@~H
Invalid "to" argument: only initial part "#1/A:609" of atom specifier valid
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central.pdb"
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> hide #!1 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> hide #!25 models
> hide #27 models
> show #27 models
> hide #27 models
> hide #29 models
> hide #30 models
> hide #32 models
> hide #31 models
> hide #33 models
> hide #34 models
> hide #35 models
> show #27 models
> show #29 models
> rmsd #27 to #29
RMSD between 22 atom pairs is 3.588
> rmsd #27 to #31
RMSD between 22 atom pairs is 3.666
> show #31 models
> hide #29 models
> show #29 models
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> show #32 models
> rmsd #27 to #32
RMSD between 22 atom pairs is 3.639
> hide #31 models
> hide #32 models
> hide #29 models
> hide #27 models
> show #27 models
> show #29 models
> hide #27 models
> show #31 models
> rmsd #29 to #31
RMSD between 22 atom pairs is 2.213
> show #27 models
> hide #27 models
> hide #29 models
> show #32 models
> show #27 models
> hide #32 models
> hide #31 models
> show #29 models
> hide #29 models
> show #29 models
> show #31 models
> hide #31 models
> show #31 models
> hide #31 models
> hide #27 models
> show #27 models
> show #31 models
> hide #31 models
> hide #27 models
> show #27 models
> hide #29 models
> show #29 models
> show #31 models
> hide #31 models
> show #31 models
> show #32 models
> hide #32 models
> show #32 models
> hide #31 models
> show #31 models
> hide #32 models
> show #32 models
> hide #29 models
> show #29 models
> hide #27 models
> hide #32 models
> show #27 models
> hide #27 models
> show #27 models
> hide #27 models
> show #27 models
> hide #27 models
> show #27 models
> hide #27 models
> show #27 models
> hide #27 models
> align #27 toAtoms #29 move nothing
RMSD between 22 atom pairs is 2.489 angstroms
> hide #29 models
> show #29 models
> align #29 toAtoms #27
RMSD between 22 atom pairs is 2.489 angstroms
> show #27 models
> show #32 models
> hide #31 models
> hide #32 models
> align #29 toAtoms #27 matchAtomNames true
Pairing dropped 22 atoms and 22 reference atoms
No atoms paired for alignment
> align #29 toAtoms #27 matchAtomNames true
Pairing dropped 22 atoms and 22 reference atoms
No atoms paired for alignment
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer.pdb"
> hide #27 models
> hide #29 models
> hide #36 models
> show #36 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer.pdb"
> hide #36 models
> hide #37 models
> show #37 models
> align #29 toAtoms #37 matchAtomNames true
RMSD between 22 atom pairs is 2.489 angstroms
> hide #37 models
> show #37 models
> show #27 models
> hide #27 models
> show #29 models
> align #29 toAtoms #37
RMSD between 22 atom pairs is 2.489 angstroms
> rmsd #29 to #37
RMSD between 22 atom pairs is 2.489
> hide #29 models
> show #31 models
> rmsd #29 to #31
RMSD between 22 atom pairs is 3.989
> align 329 to #1
Missing or invalid "atoms" argument: invalid atoms specifier
> align #29 toAtoms #1
Unequal number of atoms to pair, 22 and 6846
> align #29 toAtoms #31
RMSD between 22 atom pairs is 0.978 angstroms
> show #29 models
> hide #37 models
> view #27-37 initial
Expected an integer >= 1 or a keyword
> view initial #27-37 initial
Expected a keyword
> view initial #27-37
> align #29 toAtoms #31
RMSD between 22 atom pairs is 0.978 angstroms
> hide #31 models
> show #27 models
> hide #29 models
> show #29 models
> hide #27 models
> show #37 models
> label #22,29,37 atoms attribute name
> show #27 models
> hide #!29 models
> hide #!37 models
> label #22,27 atoms attribute name
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/docked_C2.2_renamed_atoms.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/docked_C2.2_renamed_atoms.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened docked_C2.2_renamed_atoms.pdbqt containing 1 structures (22 atoms, 23
bonds)
> hide #!27 models
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> label #22,38 atoms attribute name
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer.pdb"
> hide #!38 models
> show #!38 models
> color #39 #415bffff
> label #22,38-39 atoms attribute name
> hide #!38 models
> show #!38 models
> hide #!39 models
> show #!39 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!22 models
> color byhetero
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!39 models
> show #!39 models
> hide #!38 models
> show #!38 models
> hide #!39 models
> show #!39 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> hide #!39 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed.pdb
---
warning | Ignored bad PDB record found on line 23
> label #40 atoms attribute name
> hide #!40 models
> show #!40 models
> show #!29 models
> show #!27 models
> hide #!27 models
> rmsd #40 to 329
Invalid "to" argument: invalid atoms specifier
> rmsd #40 to #29
RMSD between 22 atom pairs is 1.561
> align #29 toAtoms #40
RMSD between 22 atom pairs is 0.880 angstroms
> view initial #29
> hide #!29 models
> show #!29 models
> rmsd #40 to #29
RMSD between 22 atom pairs is 1.250
> rmsd #40 to #31
RMSD between 22 atom pairs is 1.789
> show #31 models
> show #32 models
> view initial #29,31,32,40
> rmsd #40 to #32
RMSD between 22 atom pairs is 1.912
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central.pdb
---
warnings | Ignored bad PDB record found on line 5
Ignored bad PDB record found on line 7
Ignored bad PDB record found on line 14
> align #41 toAtoms #40
RMSD between 22 atom pairs is 2.442 angstroms
> hide #31 models
> hide #32 models
> hide #!29 models
> hide #!40 models
> show #!40 models
> hide #!40 models
> label #41 atoms attribute name
> ui mousemode right translate
> show #!40 models
> hide #!40 models
> show #!39 models
> hide #!39 models
> show #!39 models
> ui mousemode right "rotate selected models"
> select add #41
22 atoms, 23 bonds, 1 residue, 2 models selected
> view matrix models
> #41,0.94928,0.14026,-0.28142,19.492,-0.15443,0.98759,-0.028715,23.961,0.2739,0.07072,0.95915,-39.717
> view matrix models
> #41,0.94765,0.016102,-0.31891,36.963,0.020875,0.99347,0.1122,-13.564,0.31863,-0.11298,0.94112,-23.739
> view matrix models
> #41,0.99805,-0.059362,0.01954,4.9264,0.058007,0.99627,0.063845,-13.898,-0.023257,-0.062586,0.99777,9.7105
> hide #!39 models
> show #!39 models
> select subtract #41
Nothing selected
> ui mousemode right translate
> hide #!39 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!41 models
> show #!41 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!41 models
> show #!41 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!41 models
> hide #!38 models
> show #!38 models
> show #!41 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> hide #!38 models
> show #!38 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed
> copy.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed
copy.pdb
---
warning | Ignored bad PDB record found on line 23
> hide #!38 models
> rmsd #41 to #32
RMSD between 22 atom pairs is 3.628
> show #32 models
> hide #32 models
> hide #!41 models
> show #!41 models
> hide #!41 models
> show #!41 models
> rmsd #42 to #32
RMSD between 22 atom pairs is 1.755
> rmsd #42 to #29
RMSD between 22 atom pairs is 1.236
> rmsd #42 to #31
RMSD between 22 atom pairs is 1.775
> rmsd #42 to #32
RMSD between 22 atom pairs is 1.755
> hide #!41 models
> hide #42 models
> show #32 models
> show #31 models
> show #42 models
> hide #32 models
> hide #31 models
> show #!40 models
> hide #!40 models
> show #!39 models
> show #!41 models
> hide #42 models
> hide #!39 models
> hide #!41 models
> show #!41 models
> show #!39 models
> hide #!39 models
> show #!38 models
> hide #!38 models
> show #!38 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central_renamed.pdb"
> hide #43 models
> show #43 models
> hide #43 models
> show #43 models
> hide #43 models
> show #43 models
> hide #!41 models
> show #!41 models
> view #41 initial
Expected an integer >= 1 or a keyword
> view initial #1
> view initial #41
> hide #43 models
> show #43 models
> show #!1 models
> hide #43 models
> show #43 models
> hide #!41 models
> hide #!38 models
> hide #43 models
> show #43 models
> hide #!1 models
> show #!1 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central_renamed.pdb"
> hide #43 models
> show #43 models
> hide #43 models
> view #43
> view #44
> close #43
> show #42 models
> view #42
> hide #!1 models
> close #40
> close #41
> close #39
> show #!38 models
> hide #!38 models
> view #44
> show #33 models
> show #34 models
> show #35 models
> rmsd #44 to #33
RMSD between 22 atom pairs is 0.656
> rmsd #44 to #34
RMSD between 22 atom pairs is 1.290
> rmsd #44 to #35
RMSD between 22 atom pairs is 1.481
> hide #34 models
> hide #35 models
> show #35 models
> show #34 models
> hide #33 models
> hide #34 models
> show #34 models
> hide #35 models
> show #35 models
> hide #34 models
> show #34 models
> hide #35 models
> show #35 models
> hide #34 models
> hide #35 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #44 models
> show #44 models
> hide #42 models
> show #42 models
> show #!29 models
> show #31 models
> show #32 models
> hide #31 models
> hide #32 models
> label delete
> view #29
> hide HC
> view lst
Expected an objects specifier or a view name or a keyword
> view lstview ist
Expected an objects specifier or a view name or a keyword
> view list
No named views.
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/240830_zfO1_final_structures_maps_comparison_15_mutagen_extraDensity.cxs"
Opened emd_9360.map as #1, grid size 200,200,200, pixel 1.03, shown at level
3.67, step 1, values float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc as #3,
grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values float32
Opened
zfO1_C11_1mM_final_cryosparc_P120_cryosparc_P120_J2190_007_volume_map.mrc as
#4, grid size 256,256,256, pixel 1.15, shown at level 0.176, step 1, values
float32
Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map.mrc as #7, grid
size 200,200,200, pixel 1.07, shown at level 0.34, step 1, values float32
Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map_sharp.mrc as #8,
grid size 200,200,200, pixel 1.07, shown at level 0.272, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map.mrc as #11,
grid size 200,200,200, pixel 1.07, shown at level 0.289, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc as
#12, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map.mrc as #15,
grid size 200,200,200, pixel 1.04, shown at level 0.0979, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc as
#16, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 0 as
#25.1, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 1 as
#25.2, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 2 as
#25.3, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 3 as
#25.4, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 4 as
#25.5, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 5 as
#25.6, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened emd_9360.map 0 as #24.1, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 1 as #24.2, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 2 as #24.3, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 3 as #24.4, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 4 as #24.5, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 0 as
#31.1, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 1 as
#31.2, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 2 as
#31.3, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 3 as
#31.4, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 4 as
#31.5, grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 5 as
#31.6, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 0 as
#30.1, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 1 as
#30.2, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 2 as
#30.3, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 3 as
#30.4, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 4 as
#30.5, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 5 as
#30.6, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
opened ChimeraX session
> show #!3 models
> hide #!3 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Ward_lab/230323_zfO1_paper_stuff/zfOtop1_blockers_paper_2023/figures/fig3_cryoEM/final_maps_models/240807_zfO1_final_structures_maps_comparison_14.cxs"
Opened emd_9360.map as #1, grid size 200,200,200, pixel 1.03, shown at level
3.67, step 1, values float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc as #3,
grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values float32
Opened
zfO1_C11_1mM_final_cryosparc_P120_cryosparc_P120_J2190_007_volume_map.mrc as
#4, grid size 256,256,256, pixel 1.15, shown at level 0.176, step 1, values
float32
Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map.mrc as #7, grid
size 200,200,200, pixel 1.07, shown at level 0.34, step 1, values float32
Opened zfO1_NC2_1mM_final_cryosparc_P120_J3308_008_volume_map_sharp.mrc as #8,
grid size 200,200,200, pixel 1.07, shown at level 0.272, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map.mrc as #11,
grid size 200,200,200, pixel 1.07, shown at level 0.242, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc as
#12, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map.mrc as #15,
grid size 200,200,200, pixel 1.04, shown at level 0.0979, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc as
#16, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 0 as
#25.1, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 1 as
#25.2, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 2 as
#25.3, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 3 as
#25.4, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 4 as
#25.5, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened zfO1_NC2_10mM_final_cryosparc_P120_J3424_008_volume_map_sharp.mrc 5 as
#25.6, grid size 200,200,200, pixel 1.07, shown at level 0.939, step 1, values
float32
Opened emd_9360.map 0 as #24.1, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 1 as #24.2, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 2 as #24.3, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 3 as #24.4, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened emd_9360.map 4 as #24.5, grid size 200,200,200, pixel 1.03, shown at
level 3.67, step 1, values float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 0 as
#31.1, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 1 as
#31.2, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 2 as
#31.3, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 3 as
#31.4, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 4 as
#31.5, grid size 256,256,256, pixel 1.15, shown at level 0.35, step 1, values
float32
Opened zfO1_C11_1mM_final_cryosparc_P120_J2190_007_volume_map_sharp.mrc 5 as
#31.6, grid size 256,256,256, pixel 1.15, shown at level 0.266, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 0 as
#30.1, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 1 as
#30.2, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 2 as
#30.3, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 3 as
#30.4, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 4 as
#30.5, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
Opened zfO1_NC36_1mM_final_cryosparc_P120_J2922_005_volume_map_sharp.mrc 5 as
#30.6, grid size 200,200,200, pixel 1.04, shown at level 0.231, step 1, values
float32
opened ChimeraX session
> transparency 0 target ca
> select clear
> style #!13,34 stick
Changed 13056 atom styles
> hide #!13 models
> show #!13 models
> view
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_outer_renamed.pdb
---
warning | Ignored bad PDB record found on line 23
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/c2.2_cryoEM_chA_central_renamed.pdb"
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_zfO1_ADGPU_c2g_modded_-5_LGA200_run158.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_mO1_ADGPU_c2g_modded_-5_LGA200_run154.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_hO1_ADGPU_c2g_modded_-5_LGA200_run155.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_zfO1_ADGPU_central_c2g_modded_-2_run11.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_mO1_ADGPU_central_c2g_modded_-2_run19.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_centralSite_rescored/CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES C=C(C)COc1ccccc1NC(=O)c1nc[nH]c1C
Ignored bad PDB record found on line 2
REMARK SMILES IDX 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 14 15 15 16 16 17 19 18 17 19 18 20 20 21
Ignored bad PDB record found on line 4
REMARK H PARENT 12 14 18 22
Ignored bad PDB record found on line 5
REMARK INDEX MAP 6 1 7 2 8 3 9 4 10 5 11 6 5 7 4 8 2 9 1 10 3 11 12 12 13 13
15 messages similar to the above omitted
Opened CB15302368_1_C2.2_hO1_ADGPU_central_c2g_modded_-2_run12.pdbqt
containing 1 structures (22 atoms, 23 bonds)
> hide #39 models
> show #39 models
> view initial #13
> hide #!34 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/mO1_on_zfO1C2.2_clean_REDUCE_GLH274.pdbqt"
Chain information for mO1_on_zfO1C2.2_clean_REDUCE_GLH274.pdb #44
---
Chain | Description
A | No description available
Opened mO1_on_zfO1C2.2_clean_REDUCE_GLH274.pdbqt containing 1 structures (5211
atoms, 5317 bonds)
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/hO1_mO1_on_zfO1_C2.2_SWISSMODEL_dockings/best_poses_from_hmzfO1_rescored/hO1_on_zfO1C2.2_clean_REDUCE_GLH276_HIE600.pdbqt"
Chain information for hO1_on_zfO1C2.2_clean_REDUCE_GLH276_HIE600.pdb #45
---
Chain | Description
A | No description available
Opened hO1_on_zfO1C2.2_clean_REDUCE_GLH276_HIE600.pdbqt containing 1
structures (5330 atoms, 5442 bonds)
> hide #44 models
> show #44 models
> hide #45 models
> hide #44 models
> hide #!13 models
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo.pdb"
Summary of feedback from opening /Users/bburendei/Dropbox (Scripps
Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_NC2_10mM_bestModel_apo.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
3270 messages similar to the above omitted
Chain information for zfO1_NC2_10mM_bestModel_apo.pdb #46
---
Chain | Description
A B | No description available
> hide #40 models
> hide #41 models
> hide #42 models
> hide #43 models
> hide #!46 models
> show #!46 models
> color #46 #aa5ee8
> show #46/A:126,130,133,134,267,574,573,532,570
> hide /B target ca
> hide :CLR.Y01
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide :CLR,Y01
> color byhet'
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color byhetero
> hide #39 models
> show #39 models
> hide #37 models
> hide #36 models
> show #36 models
> hide #39 models
> show #40 models
> hide #38 models
> hide #36 models
> show #36 models
> color #36,37 cyan
> show #39 models
> color #36,37 cyanview list
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> view list
Named views: 570central_modelComp2, CHS_in_dens_central, CLR_in_outer_molOnly,
C_dom_pocket_mirror2docked, C_domonly_side_comparison, Cdom_pocket,
F570_central_NC36_2copies_modelComp_view, F570central_densityComp,
F570central_modelComp, F570central_modelComp2, F570central_resi_comp,
F570central_site_allModels, F570outer, F570outer_resi_comp,
F570outer_site_modelComp2, NC2_central_molOnly, NC2_outer_molOnly,
NC36_in_Dens_outer, NC36_in_dens_central, N_dom_side_comparison,
N_domonly_side_comparison, all_models_aligned_Cdompocket_models,
all_models_aligned_F570central_models,
all_models_aligned_F570outer_site_models, bottom_view, c11_in_dens_Cdom,
c11_in_dens_central, central_site_45, central_site_flatView, outer_site_45,
outer_site_NC2_flat_view, side_view, side_view_NdomAligned, side_view_models,
top_view
> view F570outer
> view F570outer_site_modelComp2
> hide #39 models
> hide #40 models
> show #40 models
> show #38 models
> hide #38 models
> show #44 models
> hide #44 models
> show #44 models
> hide #44 models
> show #45 models
> color #45 #cf7c15ff
> color #45 #cfca15ff
> color #45 #cfa815ff
> color #45 #ada815ff
> color #45 #ada81cff
> color #45 #d7a81cff
> color #45 #e9a81cff
> color #45 #eca81cff
> hide #40 models
> show #40 models
> color #40 #eca81cff
> color #40 #ec621cff
> hide #36 models
> show #36 models
> hide #45 models
> hide #!46 models
> show #!46 models
> show #45 models
> hide #!46 models
> select #45/A:132
16 atoms, 17 bonds, 1 residue, 1 model selected
> select add #45/A:135
21 atoms, 21 bonds, 2 residues, 1 model selected
> select add #45/A:136
29 atoms, 28 bonds, 3 residues, 1 model selected
> select add #45/A:280
38 atoms, 36 bonds, 4 residues, 1 model selected
> select add #45/A:139
47 atoms, 44 bonds, 5 residues, 1 model selected
> select add #45/A:276
58 atoms, 54 bonds, 6 residues, 1 model selected
> select add #45/A:596
70 atoms, 66 bonds, 7 residues, 1 model selected
> select add #45/A:599
79 atoms, 74 bonds, 8 residues, 1 model selected
> select add #45/A:600
91 atoms, 86 bonds, 9 residues, 1 model selected
> select add #45/A:603
97 atoms, 91 bonds, 10 residues, 1 model selected
> show sel
> select clear
> select #45/A:135
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #!46 models
> hide #!46 models
> show #!46 models
> hide #!46 models
> select #45/A:140
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #45/A:143
21 atoms, 20 bonds, 2 residues, 1 model selected
> show #!46 models
> hide #46
> show #46/A:126,130,133,134,267,574,573,532,570
> select clear
> select #45/A:140
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel
> hide #45 models
> show #45 models
> select #45/A:603@CB
1 atom, 1 residue, 1 model selected
> hide sle
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel
> select clear
> select #45/A:558
16 atoms, 17 bonds, 1 residue, 1 model selected
> show sel
> open "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/zfO1_C2.2_E267_protonation_test/zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdbqt"
Chain information for zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdb
#47
---
Chain | Description
A | No description available
Opened zfO1_NC2_10mM_bestModel_apo_chAclean_GLH267_REDUCE.pdbqt containing 1
structures (3755 atoms, 3831 bonds)
> hide #!47 models
> show #!47 models
> hide #47
> show #47/A:126,130,133,134,267,574,573,532,570
> color #aa5ee8
> undo
> color #47 #aa5ee8
> select clear
> hide #!46 models
> close #46
> color byhetero
> select clear
> color #40 #ecbd1cff
> color #40 #ec991cff
> color byhetero
> select clear
> size #36,40 stickRadius 0.2
Changed 46 bond radii
> size #36,40 stickRadius 0.4
Changed 46 bond radii
> size #36,40 stickRadius 0.3
Changed 46 bond radii
> color #40 #00991cff
> color #40 #00ff1cff
> color #40 lime
> color #40 #00d700ff
> color byhetero
> size #36,40 stickRadius 0.2
Changed 46 bond radii
> select clear
> size #36,40 stickRadius 0.25
Changed 46 bond radii
> size #36,40 stickRadius 0.2
Changed 46 bond radii
> select clear
> ui tool show "Side View"
> hide #!47 models
> show #!47 models
> hide #47:573
> hide #45:590
> hide #45:599
> show #38 models
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> hide #36 models
> save "/Users/bburendei/Dropbox (Scripps
> Research)/my_Forli_Lab/zfOtop1_screening/240904_hO1_mO1_outer_central_sites_NC2_docking/240906_best_poses_comparison_session.cxs"
> show #42 models
> hide #42 models
> hide #45 models
> hide #!47 models
> hide #40 models
> hide #38 models
> show #!1 models
> show #45 models
> hide #45 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> alias nice cartoon suppressBackboneDisplay false; cartoon style width 1;
> size stickRadius 0.12
> lighting soft
> nice
Changed 0 bond radii
> alias voltr5 vol transparency 0.5
> alias voltroff vol transparency 0
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> alias cartoonDefaults cartoon style protein modeh default
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 - 83.1
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: Mac
Model Identifier: Mac14,2
Model Number: Z15S000D5LL/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.6.7 (22G720)
Kernel Version: Darwin 22.6.0
Time since boot: 2 days, 10 hours, 47 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 Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL P2721Q:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
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 , 14 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 14 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Unfortunately a bug in the Qt window toolkit used by ChimeraX sometimes causes ChimeraX to crash when waking from sleep in Mac computers. This bug is in Qt 6.6 and we have not observed the crash in Qt version 6.7 which is used by the ChimeraX daily build. So you might try the ChimeraX daily build. Otherwise my only advice is to save your work before letting your computer sleep.
Mac Qt 6.6 window toolkit crash in _NSViewHierarchyDidChangeBackingProperties.
Note:
See TracTickets
for help on using tickets.
Reported by Batuujin Burendei