Context Navigation

← Previous Ticket
Next Ticket →

#6412 closed defect (can't reproduce)

Crash while running AlphaFold prediction

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

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.4.dev202202010639 (2022-02-01 06:39:28 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x000031a4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002d90 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005b8c (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004d24 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003960 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004c1c (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004bb4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005a18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00000e34 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000007b4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000022d0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005bc0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004750 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002db4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00003d20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000531c (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002e00 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000034fc (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002cec (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00001ed0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002614 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004c84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000100c (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000042cc (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00000ed4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000345c (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005844 (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\threading.py", line 930 in _bootstrap

Current thread 0x0000206c (most recent call first):
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\site-packages\chimerax\ui\gui.py", line 318 in event_loop
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.4.dev202202010639\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202202010639 (2022-02-01)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Modeller Comparative"

> ui tool show AlphaFold

> alphafold match
> MVTPLPGPEHPLLYDDFAGGGLFKQNWMNWYNQDGGSGTFIKTTEGTRSIGKFTQTPSSSSSWAKFQPMNETFDLSGYRYMNLSLQNAGYAQSLIRVVIGDGTTNYNLTGGYVPASNTWTDLQFDLDALMPKIQKKKVKLEIWLRQAGGTYGEMLIDDIVFTTASSGTAPQLSPAGMSANTDSSYNQNTNFTFEATYIDPDNEAPFAVQVIIDDIAYNMRETDQADVTYTDGKHYRFMTKLPAGAHSYYFRTSDTTSNEVNTGIQNLNVVQTSSVIDIVVSQAGYSADDVKNAKLISTTTVTDATYEILDGTTVIASGTMTYEGLYWNKHVYSIGFSDVTASGNSYRVRSNQVYSYSFEITPNLWDQYKDEMTAFYRLQRASVATSDAYPEGYSSVAPSAKLYHAAGHLDDAQSADGLTHYDLTGSWYDAGDYGKYGGNQWVGAEIALAYTRYADKDSVKYDNDSNGIPDLVDEAVFGSEYLIKFADQLGGEMYNLRNNASFVHPEKSTDNISGTADDRKLTDLSVGGSAKSAGTLAATARAIRTAINEGDIASSQIAELTDFANQCETAAVTFYNYVVANPDGPIGSYSTRGGIPNSKLLADVELYLLTGDIQYRNAATATISALTLSDISSTNYWDMSPMSMAEFYPVADAETQSHIHSLLKGQADFFLSMSDDTPYGVLNQFKNFGVNEPHASYLGDMLRYYELFGDPAALQAVVKGMYWLFGENPWNISWVSGIGTQHVMFPHTRYNEESNTAGDTGIILPGAMVSGPNMKDPKNKSSVSPWYEDRSLYLDDTNQWRYNEFSISIQAGLLYTVMGLSATPGTGVDNVAKPPALPLLSPVIGEWVRGNVTVFAQAGDQLSDVEYAATGLPYQPMTVSGNVYSTVSGAVYAAVIDESQSLPYTNRRVDVRAKDPSGAYTYSSTHYTVAPPLPDPSTPLLYDDFGGAGFWGGSAANTTWVNWYNQNGGTGTFTKLTADGRSVGKFTQVPANVNSAAKFQAWNDVVDLSGYQYLNITLKNPASPDLRTRIEIYDGKRTYNLTGGWVEVPANWSDLQFDLNALTPAIDKKALKMSIWLKQNTVTPGEMLIDEIKATNKVRGSAPTLTLGGVDQPQGTPQTEFTFTVTYTDADNQAPFTMELVLDGVVRKMQPAVPGDTNYSDGRIYQYSTKLLPGKHSYYFHTTDTFTDAVSTEVQSAPEVSLEHHHHHH

No AlphaFold model with similar sequence for 1 sequences  

Opened 0 AlphaFold model  

> alphafold predict
> MVTPLPGPEHPLLYDDFAGGGLFKQNWMNWYNQDGGSGTFIKTTEGTRSIGKFTQTPSSSSSWAKFQPMNETFDLSGYRYMNLSLQNAGYAQSLIRVVIGDGTTNYNLTGGYVPASNTWTDLQFDLDALMPKIQKKKVKLEIWLRQAGGTYGEMLIDDIVFTTASSGTAPQLSPAGMSANTDSSYNQNTNFTFEATYIDPDNEAPFAVQVIIDDIAYNMRETDQADVTYTDGKHYRFMTKLPAGAHSYYFRTSDTTSNEVNTGIQNLNVVQTSSVIDIVVSQAGYSADDVKNAKLISTTTVTDATYEILDGTTVIASGTMTYEGLYWNKHVYSIGFSDVTASGNSYRVRSNQVYSYSFEITPNLWDQYKDEMTAFYRLQRASVATSDAYPEGYSSVAPSAKLYHAAGHLDDAQSADGLTHYDLTGSWYDAGDYGKYGGNQWVGAEIALAYTRYADKDSVKYDNDSNGIPDLVDEAVFGSEYLIKFADQLGGEMYNLRNNASFVHPEKSTDNISGTADDRKLTDLSVGGSAKSAGTLAATARAIRTAINEGDIASSQIAELTDFANQCETAAVTFYNYVVANPDGPIGSYSTRGGIPNSKLLADVELYLLTGDIQYRNAATATISALTLSDISSTNYWDMSPMSMAEFYPVADAETQSHIHSLLKGQADFFLSMSDDTPYGVLNQFKNFGVNEPHASYLGDMLRYYELFGDPAALQAVVKGMYWLFGENPWNISWVSGIGTQHVMFPHTRYNEESNTAGDTGIILPGAMVSGPNMKDPKNKSSVSPWYEDRSLYLDDTNQWRYNEFSISIQAGLLYTVMGLSATPGTGVDNVAKPPALPLLSPVIGEWVRGNVTVFAQAGDQLSDVEYAATGLPYQPMTVSGNVYSTVSGAVYAAVIDESQSLPYTNRRVDVRAKDPSGAYTYSSTHYTVAPPLPDPSTPLLYDDFGGAGFWGGSAANTTWVNWYNQNGGTGTFTKLTADGRSVGKFTQVPANVNSAAKFQAWNDVVDLSGYQYLNITLKNPASPDLRTRIEIYDGKRTYNLTGGWVEVPANWSDLQFDLNALTPAIDKKALKMSIWLKQNTVTPGEMLIDEIKATNKVRGSAPTLTLGGVDQPQGTPQTEFTFTVTYTDADNQAPFTMELVLDGVVRKMQPAVPGDTNYSDGRIYQYSTKLLPGKHSYYFHTTDTFTDAVSTEVQSAPEVSLEHHHHHH
> prokaryote true

Running AlphaFold prediction  

> alphafold search
> MVTPLPGPEHPLLYDDFAGGGLFKQNWMNWYNQDGGSGTFIKTTEGTRSIGKFTQTPSSSSSWAKFQPMNETFDLSGYRYMNLSLQNAGYAQSLIRVVIGDGTTNYNLTGGYVPASNTWTDLQFDLDALMPKIQKKKVKLEIWLRQAGGTYGEMLIDDIVFTTASSGTAPQLSPAGMSANTDSSYNQNTNFTFEATYIDPDNEAPFAVQVIIDDIAYNMRETDQADVTYTDGKHYRFMTKLPAGAHSYYFRTSDTTSNEVNTGIQNLNVVQTSSVIDIVVSQAGYSADDVKNAKLISTTTVTDATYEILDGTTVIASGTMTYEGLYWNKHVYSIGFSDVTASGNSYRVRSNQVYSYSFEITPNLWDQYKDEMTAFYRLQRASVATSDAYPEGYSSVAPSAKLYHAAGHLDDAQSADGLTHYDLTGSWYDAGDYGKYGGNQWVGAEIALAYTRYADKDSVKYDNDSNGIPDLVDEAVFGSEYLIKFADQLGGEMYNLRNNASFVHPEKSTDNISGTADDRKLTDLSVGGSAKSAGTLAATARAIRTAINEGDIASSQIAELTDFANQCETAAVTFYNYVVANPDGPIGSYSTRGGIPNSKLLADVELYLLTGDIQYRNAATATISALTLSDISSTNYWDMSPMSMAEFYPVADAETQSHIHSLLKGQADFFLSMSDDTPYGVLNQFKNFGVNEPHASYLGDMLRYYELFGDPAALQAVVKGMYWLFGENPWNISWVSGIGTQHVMFPHTRYNEESNTAGDTGIILPGAMVSGPNMKDPKNKSSVSPWYEDRSLYLDDTNQWRYNEFSISIQAGLLYTVMGLSATPGTGVDNVAKPPALPLLSPVIGEWVRGNVTVFAQAGDQLSDVEYAATGLPYQPMTVSGNVYSTVSGAVYAAVIDESQSLPYTNRRVDVRAKDPSGAYTYSSTHYTVAPPLPDPSTPLLYDDFGGAGFWGGSAANTTWVNWYNQNGGTGTFTKLTADGRSVGKFTQVPANVNSAAKFQAWNDVVDLSGYQYLNITLKNPASPDLRTRIEIYDGKRTYNLTGGWVEVPANWSDLQFDLNALTPAIDKKALKMSIWLKQNTVTPGEMLIDEIKATNKVRGSAPTLTLGGVDQPQGTPQTEFTFTVTYTDADNQAPFTMELVLDGVVRKMQPAVPGDTNYSDGRIYQYSTKLLPGKHSYYFHTTDTFTDAVSTEVQSAPEVSLEHHHHHH

ChimeraX REST job id:
JF6WH571NSY95BMAAW2YEC6ESDY9MD5IG9P6FEJJF1T25EK96IHG12DX89AVOFQ8  

> alphafold search
> MVTPLPGPEHPLLYDDFAGGGLFKQNWMNWYNQDGGSGTFIKTTEGTRSIGKFTQTPSSSSSWAKFQPMNETFDLSGYRYMNLSLQNAGYAQSLIRVVIGDGTTNYNLTGGYVPASNTWTDLQFDLDALMPKIQKKKVKLEIWLRQAGGTYGEMLIDDIVFTTASSGTAPQLSPAGMSANTDSSYNQNTNFTFEATYIDPDNEAPFAVQVIIDDIAYNMRETDQADVTYTDGKHYRFMTKLPAGAHSYYFRTSDTTSNEVNTGIQNLNVVQTSSVIDIVVSQAGYSADDVKNAKLISTTTVTDATYEILDGTTVIASGTMTYEGLYWNKHVYSIGFSDVTASGNSYRVRSNQVYSYSFEITPNLWDQYKDEMTAFYRLQRASVATSDAYPEGYSSVAPSAKLYHAAGHLDDAQSADGLTHYDLTGSWYDAGDYGKYGGNQWVGAEIALAYTRYADKDSVKYDNDSNGIPDLVDEAVFGSEYLIKFADQLGGEMYNLRNNASFVHPEKSTDNISGTADDRKLTDLSVGGSAKSAGTLAATARAIRTAINEGDIASSQIAELTDFANQCETAAVTFYNYVVANPDGPIGSYSTRGGIPNSKLLADVELYLLTGDIQYRNAATATISALTLSDISSTNYWDMSPMSMAEFYPVADAETQSHIHSLLKGQADFFLSMSDDTPYGVLNQFKNFGVNEPHASYLGDMLRYYELFGDPAALQAVVKGMYWLFGENPWNISWVSGIGTQHVMFPHTRYNEESNTAGDTGIILPGAMVSGPNMKDPKNKSSVSPWYEDRSLYLDDTNQWRYNEFSISIQAGLLYTVMGLSATPGTGVDNVAKPPALPLLSPVIGEWVRGNVTVFAQAGDQLSDVEYAATGLPYQPMTVSGNVYSTVSGAVYAAVIDESQSLPYTNRRVDVRAKDPSGAYTYSSTHYTVAPPLPDPSTPLLYDDFGGAGFWGGSAANTTWVNWYNQNGGTGTFTKLTADGRSVGKFTQVPANVNSAAKFQAWNDVVDLSGYQYLNITLKNPASPDLRTRIEIYDGKRTYNLTGGWVEVPANWSDLQFDLNALTPAIDKKALKMSIWLKQNTVTPGEMLIDEIKATNKVRGSAPTLTLGGVDQPQGTPQTEFTFTVTYTDADNQAPFTMELVLDGVVRKMQPAVPGDTNYSDGRIYQYSTKLLPGKHSYYFHTTDTFTDAVSTEVQSAPEVSLEHHHHHH

BlastProtein finished.  
ChimeraX REST job id:
VBDDX3Y7LM0MR5G0D85KGVD1J1BBYV9HAMCNE6BRIS7VGF81KMKS0KMPFQ9LEW8Y  
Parsing BLAST results.  

> alphafold fetch CELK_ACET2 version 2

Fetching compressed AlphaFold A3DCH1 from
https://alphafold.ebi.ac.uk/files/AF-A3DCH1-F1-model_v2.cif  
Chain information for AlphaFold CELK_ACET2 #1  
---  
Chain | Description | UniProt  
A | Cellulose 1,4-beta-cellobiosidase | CELK_HUNT2  
  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
CELK_ACET2 | MVTPL...HHHHH | 2.9 | 3.6  

> alphafold fetch CELK_ACET2 version 2

| Chain information for AlphaFold CELK_ACET2 #2  
---  
Chain | Description | UniProt  
A | Cellulose 1,4-beta-cellobiosidase | CELK_HUNT2  
  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
CELK_ACET2 | MVTPL...HHHHH | 2.9 | 3.6  
BlastProtein finished.  
Parsing BLAST results.  

> alphafold predict
> MVTPLPGPEHPLLYDDFAGGGLFKQNWMNWYNQDGGSGTFIKTTEGTRSIGKFTQTPSSSSSWAKFQPMNETFDLSGYRYMNLSLQNAGYAQSLIRVVIGDGTTNYNLTGGYVPASNTWTDLQFDLDALMPKIQKKKVKLEIWLRQAGGTYGEMLIDDIVFTTASSGTAPQLSPAGMSANTDSSYNQNTNFTFEATYIDPDNEAPFAVQVIIDDIAYNMRETDQADVTYTDGKHYRFMTKLPAGAHSYYFRTSDTTSNEVNTGIQNLNVVQTSSVIDIVVSQAGYSADDVKNAKLISTTTVTDATYEILDGTTVIASGTMTYEGLYWNKHVYSIGFSDVTASGNSYRVRSNQVYSYSFEITPNLWDQYKDEMTAFYRLQRASVATSDAYPEGYSSVAPSAKLYHAAGHLDDAQSADGLTHYDLTGSWYDAGDYGKYGGNQWVGAEIALAYTRYADKDSVKYDNDSNGIPDLVDEAVFGSEYLIKFADQLGGEMYNLRNNASFVHPEKSTDNISGTADDRKLTDLSVGGSAKSAGTLAATARAIRTAINEGDIASSQIAELTDFANQCETAAVTFYNYVVANPDGPIGSYSTRGGIPNSKLLADVELYLLTGDIQYRNAATATISALTLSDISSTNYWDMSPMSMAEFYPVADAETQSHIHSLLKGQADFFLSMSDDTPYGVLNQFKNFGVNEPHASYLGDMLRYYELFGDPAALQAVVKGMYWLFGENPWNISWVSGIGTQHVMFPHTRYNEESNTAGDTGIILPGAMVSGPNMKDPKNKSSVSPWYEDRSLYLDDTNQWRYNEFSISIQAGLLYTVMGLSATPGTGVDNVAKPPALPLLSPVIGEWVRGNVTVFAQAGDQLSDVEYAATGLPYQPMTVSGNVYSTVSGAVYAAVIDESQSLPYTNRRVDVRAKDPSGAYTYSSTHYTVAPPLPDPSTPLLYDDFGGAGFWGGSAANTTWVNWYNQNGGTGTFTKLTADGRSVGKFTQVPANVNSAAKFQAWNDVVDLSGYQYLNITLKNPASPDLRTRIEIYDGKRTYNLTGGWVEVPANWSDLQFDLNALTPAIDKKALKMSIWLKQNTVTPGEMLIDEIKATNKVRGSAPTLTLGGVDQPQGTPQTEFTFTVTYTDADNQAPFTMELVLDGVVRKMQPAVPGDTNYSDGRIYQYSTKLLPGKHSYYFHTTDTFTDAVSTEVQSAPEVSLEHHHHHH

Running AlphaFold prediction  


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

Log:
UCSF ChimeraX version: 1.4.dev202202010639 (2022-02-01)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.14761 Core Profile Forward-Compatible Context 21.30.40.04 30.0.13040.4003
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Locale: zh_CN.cp1252
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: windows

Manufacturer: LENOVO
Model: 20T9S1JR00
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 16,348,794,880
MaxProcessMemory: 137,438,953,344
CPU: 6 AMD Ryzen 5 4500U with Radeon Graphics         
OSLanguage: de-DE

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.5.2
    charset-normalizer: 2.0.11
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.34
    ChimeraX-AtomicLibrary: 5.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202202010639
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.6
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.1
    ChimeraX-ModelPanel: 1.3.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.8
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.7.5
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.16
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.5.1
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.3
    filelock: 3.4.2
    fonttools: 4.29.0
    funcparserlib: 1.0.0a0
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.26
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.0.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.4
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.0
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.26
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 303
    pyzmq: 22.3.0
    qtconsole: 5.2.2
    QtPy: 2.0.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    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
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.8
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component:	Unassigned → Structure Prediction
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Crash while running AlphaFold prediction

comment:2 by Tom Goddard, 4 years ago

Resolution:	→ can't reproduce
Status:	assigned → closed

Probably a Qt html widget crash in Qt 5.15. Hope that Qt 6 fixes it.

Note: See TracTickets for help on using tickets.

Download in other formats: