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Opened 3 years ago
Closed 3 years ago
#8727 closed defect (can't reproduce)
AlphaFold: Downloaded prediction file not found
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000029c02b000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000029b01f000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000029a013000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000000299007000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028f68f000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028e683000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028d677000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028c66b000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028b65f000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028a653000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000017f00b000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000017dfff000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000017cff3000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001f6f88140 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2301 in destroy
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2165 in _destroy
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 772 in remove_tool
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 335 in remove_tool
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 639 in close_request
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2267 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-03-26 23:49:49.00 +0200","app_version":"1.5.0","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.2.1 (22D68)","roots_installed":0,"name":"ChimeraX","incident_id":"67EFA668-CED1-4C59-A3C3-4E47EEFEAA33"}
{
"uptime" : 95000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 13076,
"osVersion" : {
"train" : "macOS 13.2.1",
"build" : "22D68",
"releaseType" : "User"
},
"captureTime" : "2023-03-26 23:49:40.7847 +0200",
"incident" : "67EFA668-CED1-4C59-A3C3-4E47EEFEAA33",
"pid" : 13798,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-03-26 17:28:17.1745 +0200",
"procStartAbsTime" : 1742845270748,
"procExitAbsTime" : 2292051457444,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"A212A430-4CCD-57D9-92FA-6C04921B2C96","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5A1DD3F1-670F-9E84-AA83-88187A09755E",
"throttleTimeout" : 2147483647,
"wakeTime" : 24813,
"sleepWakeUUID" : "BAED3460-D638-460A-9158-63591B4A425D",
"sip" : "enabled",
"vmRegionInfo" : "0x153c852bf448 is not in any region. Bytes after previous region: 22868640134217 Bytes before following region: 82203439795128\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, 0x0000153c852bf448","rawCodes":[1,23349676471368],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000153c852bf448"},
"vmregioninfo" : "0x153c852bf448 is not in any region. Bytes after previous region: 22868640134217 Bytes before following region: 82203439795128\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" : [{"triggered":true,"id":777952,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6906091085},{"value":5503450136},{"value":12837079000559497328},{"value":6091599968},{"value":5116282962},{"value":17062250018481102861},{"value":17062250010127589709},{"value":78},{"value":0},{"value":49},{"value":2045},{"value":2652912451},{"value":2650813097},{"value":328},{"value":8520644312},{"value":0},{"value":11},{"value":8438448448,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8438448672,"symbolLocation":224,"symbol":"_main_thread"},{"value":0},{"value":1},{"value":1},{"value":6147338728},{"value":4383977776,"symbolLocation":0,"symbol":"cfunction_call"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6905912556},"cpsr":{"value":1073745920},"fp":{"value":5503449936},"sp":{"value":5503449904},"esr":{"value":1442840704,"description":" Address size 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"name" : "libqcocoa.dylib"
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"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
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"name" : "dyld"
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"name" : "_queue.cpython-39-darwin.so"
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"arch" : "arm64",
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"size" : 32768,
"uuid" : "ff7d40db-95e6-320a-b57f-faed8f2333d9",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/select.cpython-39-darwin.so",
"name" : "select.cpython-39-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
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},
{
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"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=3.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 2944K 4 \nCG image 720K 32 \nColorSync 576K 28 \nCoreAnimation 400K 18 \nCoreGraphics 32K 2 \nCoreUI image data 4112K 33 \nFoundation 64K 2 \nKernel Alloc Once 1424K 4 \nMALLOC 1.4G 231 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 832.0M 9 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 96K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 800K 50 \nStack 385.7M 51 \nStack Guard 56.0M 1 \nVM_ALLOCATE 316.1M 402 \nVM_ALLOCATE (reserved) 192.0M 3 reserved VM address space (unallocated)\n__AUTH 1944K 365 \n__AUTH_CONST 25.0M 593 \n__CTF 756 1 \n__DATA 19.9M 724 \n__DATA_CONST 37.3M 732 \n__DATA_DIRTY 1994K 233 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 795.5M 138 \n__OBJC_CONST 4787K 329 \n__OBJC_RO 65.5M 1 \n__OBJC_RW 1988K 1 \n__TEXT 805.7M 753 \ndyld private memory 416K 3 \nmapped file 258.5M 92 \nshared memory 3264K 28 \n=========== ======= ======= \nTOTAL 5.4G 4887 \nTOTAL, minus reserved VM space 4.2G 4887 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000255
},
{
"rolloutId" : "63a0a6cfd1cdb67d083006d0",
"factorPackIds" : {
},
"deploymentId" : 240000003
}
],
"experiments" : [
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold predict
> MSTLQRRRVNRADSGDTSSIHSSANNTKGDKIANIAVDGDDDNGTNKKIAYDPEESKLRDNINIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDMLL,MSTLQRRRVNRADSGDTSSIHSSANNTKGDKIANIAVDGDDDNGTNKKIAYDPEESKLRDNINIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDMLL,MSTLQRRRVNRADSGDTSSIHSSANNTKGDKIANIAVDGDDDNGTNKKIAYDPEESKLRDNINIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDMLL,MSTLQRRRVNRADSGDTSSIHSSANNTKGDKIANIAVDGDDDNGTNKKIAYDPEESKLRDNINIPTLTLMEEVLLMGLRDREGYLSFWNDSISYALRGCIIIELALRGKIRILDDSARKRFDLSERLIEVIDSSKTGEVLLDETLQLMKNDEPLSISNWIDLLSGETWNLLKINYQLKQVRERLAKGLVDKGVLRTEMKNFFLFDMATHPIADASCKEAIKRRVLSVLVSRNMELSYNEYFPETTSFKIIRTLALICGSYGANVLENVLTTLEYEKRDKAISRAEEIMAQFSQYPFDLEKETELGVSVNLNKEVKEEIENNPGHDLQLEVIAGVFEVFSRMDMLL
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/fearjuan/Downloads/ChimeraX/AlphaFold/prediction_4
> open
> /Users/fearjuan/Downloads/ChimeraX/AlphaFold/prediction_4/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
B C D E | No description available
> alphafold predict
> MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK
> directory /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer
Downloaded prediction file not found:
/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/best_model.pdb
> alphafold predict
> MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK
> directory /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer
Downloaded prediction file not found:
/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/best_model.pdb
> alphafold predict
> MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK
> directory
> /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer
Running AlphaFold prediction
AlphaFold prediction finished
Results in
/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer
Downloaded prediction file not found:
/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer/best_model.pdb
> alphafold predict
> MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK,MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRERLAKNLVEKGVPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALIYLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK
> directory
> /Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer
Running AlphaFold prediction
> open
> "/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results
> (1)/af564_unrelaxed_rank_1_model_2.pdb"
Chain information for af564_unrelaxed_rank_1_model_2.pdb #2
---
Chain | Description
B C | No description available
> open
> "/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results
> (1)/af564_unrelaxed_rank_2_model_5.pdb"
Chain information for af564_unrelaxed_rank_2_model_5.pdb #3
---
Chain | Description
B C | No description available
> open
> "/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results
> (1)/af564_unrelaxed_rank_3_model_3.pdb"
Chain information for af564_unrelaxed_rank_3_model_3.pdb #4
---
Chain | Description
B C | No description available
> open
> "/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results
> (1)/af564_unrelaxed_rank_4_model_4.pdb"
Chain information for af564_unrelaxed_rank_4_model_4.pdb #5
---
Chain | Description
B C | No description available
> open
> "/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results
> (1)/af564_unrelaxed_rank_5_model_1.pdb"
Chain information for af564_unrelaxed_rank_5_model_1.pdb #6
---
Chain | Description
B C | No description available
> open
> "/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpindimer/results
> (1)/best_model.pdb"
Chain information for best_model.pdb #7
---
Chain | Description
B C | No description available
> hide #1 models
> ui mousemode right zoom
> ui mousemode right rotate
> ui mousemode right translate
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> coulombic #7
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_B SES surface #7.1: minimum, -15.27, mean
-1.39, maximum 14.62
Coulombic values for best_model.pdb_C SES surface #7.2: minimum, -15.65, mean
-1.42, maximum 17.07
To also show corresponding color key, enter the above coulombic command and
add key true
> color #!7 byhetero
> color #!7 bychain
> coulombic #!7
Coulombic values for best_model.pdb_B SES surface #7.1: minimum, -15.27, mean
-1.39, maximum 14.62
Coulombic values for best_model.pdb_C SES surface #7.2: minimum, -15.65, mean
-1.42, maximum 17.07
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp #!7
Map values for surface "best_model.pdb_B SES surface": minimum -27.01, mean
-6.046, maximum 23.08
Map values for surface "best_model.pdb_C SES surface": minimum -27.29, mean
-6.069, maximum 24.22
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic #!7
Coulombic values for best_model.pdb_B SES surface #7.1: minimum, -15.27, mean
-1.39, maximum 14.62
Coulombic values for best_model.pdb_C SES surface #7.2: minimum, -15.65, mean
-1.42, maximum 17.07
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #7.1 models
> hide #7.2 models
> show #7.1 models
> show #7.2 models
> color #!7 bychain
> coulombic #!7
Coulombic values for best_model.pdb_B SES surface #7.1: minimum, -15.27, mean
-1.39, maximum 14.62
Coulombic values for best_model.pdb_C SES surface #7.2: minimum, -15.65, mean
-1.42, maximum 17.07
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #7.1 models
> hide #7.2 models
> hide #!7 atoms
> hide #!7 cartoons
> show #!7 surfaces
> hide #7.1 models
> show #7.1 models
> hide #!7 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> show #3 models
> coulombic #3
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for af564_unrelaxed_rank_2_model_5.pdb_B SES surface #3.1:
minimum, -19.91, mean -0.94, maximum 12.04
Coulombic values for af564_unrelaxed_rank_2_model_5.pdb_C SES surface #3.2:
minimum, -15.68, mean -1.26, maximum 12.23
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 models
> show #2 models
> coulombic #2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for af564_unrelaxed_rank_1_model_2.pdb_B SES surface #2.1:
minimum, -15.27, mean -1.39, maximum 14.62
Coulombic values for af564_unrelaxed_rank_1_model_2.pdb_C SES surface #2.2:
minimum, -15.65, mean -1.42, maximum 17.07
To also show corresponding color key, enter the above coulombic command and
add key true
> color bfactor #!2
4470 atoms, 564 residues, 2 surfaces, atom bfactor range 17.3 to 98.8
> mlp #!2
Map values for surface "af564_unrelaxed_rank_1_model_2.pdb_B SES surface":
minimum -27.01, mean -6.046, maximum 23.08
Map values for surface "af564_unrelaxed_rank_1_model_2.pdb_C SES surface":
minimum -27.29, mean -6.069, maximum 24.22
To also show corresponding color key, enter the above mlp command and add key
true
> rainbow #!2
> color #!2 bypolymer
> color #!2 bychain
> color #!2 byhetero
> color #!2 bynucleotide
> hide #!2 models
> hide #7.1 models
> hide #7.2 models
AlphaFold prediction finished
Results in
/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer
Downloaded prediction file not found:
/Users/fearjuan/Downloads/ChimeraX/AlphaFold/GOLPH3wohairpintetramer/best_model.pdb
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGQ3SM/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 3 jours, 9 heures et 46 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Prediction |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → AlphaFold: Downloaded prediction file not found |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Would be great if we could track down the removeDockWidget() Qt crash. We have 55 reports of a crash in that call.
The missing best_model.pdb from AlphaFold probably is because the AlphaFold job failed. I think that should not download the results. But maybe the user downloaded files using the menus on the Google Colab page resulting in that missing file error. At any rate, it is almost certainly unrelated to the crash.
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Plus a crash as a tool was closed