Opened 3 years ago
Closed 3 years ago
#7141 closed defect (can't reproduce)
Crash running AlphaFold prediction
Reported by: | 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: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Thread 0x000070002f233000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x000070002e230000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x000070002d22d000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x000070002c22a000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x000070002b227000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x000070002a224000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x0000700029221000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x000070002821e000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x000070002721b000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x0000700026218000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x00007000179e5000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x0000700022a06000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x0000700021a03000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap Thread 0x0000700020a00000 (most recent call first): File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait File "/private/var/folders/tj/8gb0qd5d4_13r4qjl12943180000gr/T/AppTranslocation/B1D08FAA-D4E7-423E-A06D-FD063785058C/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates File 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has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold > help help:quickstart > alphafold predict > MPITRTGLPHAVASTSQTQETSQASASQGVLDPGTVPPRRAETFDGLSALPNDLRREIAQRCGPRSLVRLGSVSRQMAEDTRDVRAFLTARPRYDPSLEFGDVHSAESMRVALDEVTHFPYPDDEDRSEQILRGYGRLAARIPSLPQAQRFEAFTAVLNHATRHSGNMAFRVVARLTDDLGCLPEDLRALAFHAILPSLIATRRQALQAAAGAAHVGHIGAVAEADAGGVQGDGEPGPQGAVAPAQGGAAGGIGGALPFNLLASAIRHLPEEAVNLAITEAAALQTGPRLLAEVTLRLHLVGLEPIHRFQQAYAQLAEHLARSGDGAEALTHLVALLNRLPNPGVRQAAFRELTRAVHALDSTESGAAVLRRLAGALPHQPAAVRYLCSLDVLAAAASLFPSEQIPVIAAVRAQAAAIPNQAAELIARCDDAIATASMMLATVSRRYMDM Running AlphaFold prediction > alphafold predict > MPITRTGLPHAVASTSQTQETSQASASQGVLDPGTVPPRRAETFDGLSALPNDLRREIAQRCGPRSLVRLGSVSRQMAEDTRDVRAFLTARPRYDPSLEFGDVHSAESMRVALDEVTHFPYPDDEDRSEQILRGYGRLAARIPSLPQAQRFEAFTAVLNHATRHSGNMAFRVVARLTDDLGCLPEDLRALAFHAILPSLIATRRQALQAAAGAAHVGHIGAVAEADAGGVQGDGEPGPQGAVAPAQGGAAGGIGGALPFNLLASAIRHLPEEAVNLAITEAAALQTGPRLLAEVTLRLHLVGLEPIHRFQQAYAQLAEHLARSGDGAEALTHLVALLNRLPNPGVRQAAFRELTRAVHALDSTESGAAVLRRLAGALPHQPAAVRYLCSLDVLAAAASLFPSEQIPVIAAVRAQAAAIPNQAAELIARCDDAIATASMMLATVSRRYMDM Running AlphaFold prediction > show # target m Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > alphafold search > MPITRTGLPHAVASTSQTQETSQASASQGVLDPGTVPPRRAETFDGLSALPNDLRREIAQRCGPRSLVRLGSVSRQMAEDTRDVRAFLTARPRYDPSLEFGDVHSAESMRVALDEVTHFPYPDDEDRSEQILRGYGRLAARIPSLPQAQRFEAFTAVLNHATRHSGNMAFRVVARLTDDLGCLPEDLRALAFHAILPSLIATRRQALQAAAGAAHVGHIGAVAEADAGGVQGDGEPGPQGAVAPAQGGAAGGIGGALPFNLLASAIRHLPEEAVNLAITEAAALQTGPRLLAEVTLRLHLVGLEPIHRFQQAYAQLAEHLARSGDGAEALTHLVALLNRLPNPGVRQAAFRELTRAVHALDSTESGAAVLRRLAGALPHQPAAVRYLCSLDVLAAAASLFPSEQIPVIAAVRAQAAAIPNQAAELIARCDDAIATASMMLATVSRRYMDM Webservices job id: CWRZQ0HIE2C6KSGO > alphafold search > MPITRTGLPHAVASTSQTQETSQASASQGVLDPGTVPPRRAETFDGLSALPNDLRREIAQRCGPRSLVRLGSVSRQMAEDTRDVRAFLTARPRYDPSLEFGDVHSAESMRVALDEVTHFPYPDDEDRSEQILRGYGRLAARIPSLPQAQRFEAFTAVLNHATRHSGNMAFRVVARLTDDLGCLPEDLRALAFHAILPSLIATRRQALQAAAGAAHVGHIGAVAEADAGGVQGDGEPGPQGAVAPAQGGAAGGIGGALPFNLLASAIRHLPEEAVNLAITEAAALQTGPRLLAEVTLRLHLVGLEPIHRFQQAYAQLAEHLARSGDGAEALTHLVALLNRLPNPGVRQAAFRELTRAVHALDSTESGAAVLRRLAGALPHQPAAVRYLCSLDVLAAAASLFPSEQIPVIAAVRAQAAAIPNQAAELIARCDDAIATASMMLATVSRRYMDM Webservices job id: XUDWYVGJY20BWULC BLAST search returned no results. > help help:user/tools/alphafold.html > alphafold predict > MPITRTGLPHAVASTSQTQETSQASASQGVLDPGTVPPRRAETFDGLSALPNDLRREIAQRCGPRSLVRLGSVSRQMAEDTRDVRAFLTARPRYDPSLEFGDVHSAESMRVALDEVTHFPYPDDEDRSEQILRGYGRLAARIPSLPQAQRFEAFTAVLNHATRHSGNMAFRVVARLTDDLGCLPEDLRALAFHAILPSLIATRRQALQAAAGAAHVGHIGAVAEADAGGVQGDGEPGPQGAVAPAQGGAAGGIGGALPFNLLASAIRHLPEEAVNLAITEAAALQTGPRLLAEVTLRLHLVGLEPIHRFQQAYAQLAEHLARSGDGAEALTHLVALLNRLPNPGVRQAAFRELTRAVHALDSTESGAAVLRRLAGALPHQPAAVRYLCSLDVLAAAASLFPSEQIPVIAAVRAQAAAIPNQAAELIARCDDAIATASMMLATVSRRYMDM Running AlphaFold prediction ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.8.54 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac18,3 Processor Name: Quad-Core Intel Core i7 Processor Speed: 4.2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 451.120.7.0.0 OS Loader Version: 540.120.3~6 SMC Version (system): 2.41f2 Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 4 days 2:18 Graphics/Displays: Radeon Pro 580: Chipset Model: Radeon Pro 580 Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c0 ROM Revision: 113-D000AA-931 VBIOS Version: 113-D0001A1X-025 EFI Driver Version: 01.00.931 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 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: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 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: 1.1 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: 1.2 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: 1.1.1 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: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 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: 1.9 ChimeraX-PDB: 2.6.6 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: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 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: 1.8 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: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 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: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 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: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 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: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0
Change History (2)
comment:1 by , 3 years ago
Component: | Unassigned → Structure Prediction |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Crash running AlphaFold prediction |
comment:2 by , 3 years ago
Resolution: | → can't reproduce |
---|---|
Status: | assigned → closed |
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Probable crash in Qt html panel for AlphaFold.