id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7293 Graphics crash, macOS 12.3.1, Intel Iris Plus Graphics chimerax-bug-report@… Tom Goddard "{{{ 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: Aborted Thread 0x0000700024f3d000 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700023f3a000 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700022f37000 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700021f34000 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x0000700020f31000 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001ff2e000 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001ef2b000 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001df28000 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001cf25000 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000070001bf22000 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File 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""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/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/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x0000000108032600 (most recent call first): File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 235 in swap_buffers File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 496 in swap_buffers File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 179 in draw File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 73 in draw_new_frame File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 139 in _redraw_timer_callback File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 318 in event_loop File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 870 in init File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1021 in File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/private/var/folders/h0/lj8pv4t17ylcs6tvvf43fvk80000gn/T/AppTranslocation/0723B633-F18B-465E-A14C-7021C53F58EE/d/ChimeraX-1.4.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"":""2022-07-17 15:52:45.00 -0400"",""app_version"":""1.4.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.4.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.3.1 (21E258)"",""incident_id"":""C7D92BD3-04F8-48D4-AF50-98A5DD9290F5"",""name"":""ChimeraX""} { ""uptime"" : 86000, ""procLaunch"" : ""2022-07-17 14:28:56.9361 -0400"", ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,2"", ""procStartAbsTime"" : 81943216568411, ""coalitionID"" : 7724, ""osVersion"" : { ""train"" : ""macOS 12.3.1"", ""build"" : ""21E258"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2022-07-17 15:52:33.8787 -0400"", ""incident"" : ""C7D92BD3-04F8-48D4-AF50-98A5DD9290F5"", ""bug_type"" : ""309"", ""pid"" : 47373, ""procExitAbsTime"" : 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""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""6267122541fbd3022330c3ea"" }, ""deploymentId"" : 240000176 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache 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 > help help:quickstart > open > /Users/alexiavo/Downloads/DOZIPfIF4E_AF2_tempmode_none_eb419_relaxed_rank_1_model_1.pdb Chain information for DOZIPfIF4E_AF2_tempmode_none_eb419_relaxed_rank_1_model_1.pdb #1 --- Chain | Description A | No description available B | No description available > open > /Users/alexiavo/Downloads/DOZIPfIF4E_AF2_tempmode_none_eb419_relaxed_rank_5_model_5.pdb Chain information for DOZIPfIF4E_AF2_tempmode_none_eb419_relaxed_rank_5_model_5.pdb #2 --- Chain | Description A | No description available B | No description available > hide #2 models > open > /Users/alexiavo/Downloads/DOZIPfIF4E_AF2_tempmode_none_eb419_unrelaxed_rank_3_model_2.pdb Chain information for DOZIPfIF4E_AF2_tempmode_none_eb419_unrelaxed_rank_3_model_2.pdb #3 --- Chain | Description B | No description available C | No description available > hide #3 models > hide #1 models > open > /Users/alexiavo/Downloads/DOZIPfIF4E_AF2_tempmode_none_eb419_unrelaxed_rank_1_model_1.pdb Chain information for DOZIPfIF4E_AF2_tempmode_none_eb419_unrelaxed_rank_1_model_1.pdb #4 --- Chain | Description B | No description available C | No description available > hide #4 models > show #1 models > sequence chain #4/B Alignment identifier is 4/B > select #4/B:1-433 3469 atoms, 3532 bonds, 433 residues, 1 model selected > select #4/B:1-433 3469 atoms, 3532 bonds, 433 residues, 1 model selected > select add #4 5372 atoms, 5484 bonds, 660 residues, 1 model selected > select subtract #4 Nothing selected > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected Alignment identifier is 1 Alignment identifier is 2 > select /A:1-433 14002 atoms, 14128 bonds, 866 residues, 2 models selected > select /B:1-227 11140 atoms, 11290 bonds, 908 residues, 4 models selected > select /A:1-433 14002 atoms, 14128 bonds, 866 residues, 2 models selected > sequence chain #1/A Alignment identifier is 1/A > sequence chain #1/B Alignment identifier is 1/B > color #1 #40d7a9 transparency 0 > color #1 #8ed6d7 transparency 0 > undo > show #3 models > hide #3 models > show #2 models > hide #2 models > show #2 models > hide #2 models > select add #1 17791 atoms, 17966 bonds, 1093 residues, 2 models selected > select subtract #1 7001 atoms, 7064 bonds, 433 residues, 1 model selected > select add #1 17791 atoms, 17966 bonds, 1093 residues, 2 models selected > select subtract #1 7001 atoms, 7064 bonds, 433 residues, 1 model selected > select /A:1-433 14002 atoms, 14128 bonds, 866 residues, 2 models selected > color (#1 & sel) hot pink > select /B:1-227 11140 atoms, 11290 bonds, 908 residues, 4 models selected > select /B:1-227 11140 atoms, 11290 bonds, 908 residues, 4 models selected > select add #1 18141 atoms, 18354 bonds, 1341 residues, 4 models selected > select subtract #1 7351 atoms, 7452 bonds, 681 residues, 3 models selected > select /A:1-433 14002 atoms, 14128 bonds, 866 residues, 2 models selected > select /A:1-433 14002 atoms, 14128 bonds, 866 residues, 2 models selected > select add #1 17791 atoms, 17966 bonds, 1093 residues, 2 models selected > select add #2 21580 atoms, 21804 bonds, 1320 residues, 2 models selected > select subtract #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #2 Nothing selected > sequence chain #1/A Alignment identifier is 1/A > select > #1/A:34-39,52-55,62-65,69-77,85-95,110-121,138-151,168-176,186-194,211-214,220-229,245-254,281-283,285-294,307-319,333-344,355-357,378-387,390-392,404-416,429-431 2930 atoms, 2937 bonds, 172 residues, 1 model selected > select > #1/A:100-103,131-134,159-162,181-184,205-209,235-240,259-262,272-278,299-303,324-327,350-353,366-371,395-401 1037 atoms, 1032 bonds, 64 residues, 1 model selected > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select /B:1-227 11140 atoms, 11290 bonds, 908 residues, 4 models selected > sequence chain #1/B Alignment identifier is 1/B > hide #1 models > show #1 models > select add #1 18141 atoms, 18354 bonds, 1341 residues, 4 models selected > select subtract #1 7351 atoms, 7452 bonds, 681 residues, 3 models selected > select add #2 14352 atoms, 14516 bonds, 1114 residues, 3 models selected > select subtract #2 3562 atoms, 3614 bonds, 454 residues, 2 models selected > select add #2 14352 atoms, 14516 bonds, 1114 residues, 3 models selected > select subtract #2 3562 atoms, 3614 bonds, 454 residues, 2 models selected > sequence chain #1/A Alignment identifier is 1/A > select > #1/A:34-39,52-55,62-65,69-77,85-95,110-121,138-151,168-176,186-194,211-214,220-229,245-254,281-283,285-294,307-319,333-344,355-357,378-387,390-392,404-416,429-431 2930 atoms, 2937 bonds, 172 residues, 1 model selected > rainbow sel > undo > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select /A:1-433 14002 atoms, 14128 bonds, 866 residues, 2 models selected > rainbow sel & #1 > undo > select add #1 17791 atoms, 17966 bonds, 1093 residues, 2 models selected > select subtract #1 7001 atoms, 7064 bonds, 433 residues, 1 model selected > sequence chain #1/B Alignment identifier is 1/B > close #1 > undo Undo failed, probably because structures have been modified. > open > /Users/alexiavo/Downloads/DOZIPfIF4E_AF2_tempmode_none_eb419_relaxed_rank_1_model_1.pdb Chain information for DOZIPfIF4E_AF2_tempmode_none_eb419_relaxed_rank_1_model_1.pdb #1 --- Chain | Description A | No description available B | No description available > select #1/A:1-433 7001 atoms, 7064 bonds, 433 residues, 1 model selected > color sel hot pink > select #1/B:1-227 3789 atoms, 3838 bonds, 227 residues, 1 model selected > color sel cyan > color sel light sea green > sequence chain #1/B Alignment identifier is 1/B > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select #1/B:226-227 42 atoms, 42 bonds, 2 residues, 1 model selected > select #1/B:1-227 3789 atoms, 3838 bonds, 227 residues, 1 model selected > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select #1/A:1-433 7001 atoms, 7064 bonds, 433 residues, 1 model selected > sequence chain #1/A Alignment identifier is 1/A > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select #1/A:1 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:1-270 4336 atoms, 4370 bonds, 270 residues, 1 model selected > select #1/A:1-2 30 atoms, 29 bonds, 2 residues, 1 model selected > select #1/A:1-260 4166 atoms, 4200 bonds, 260 residues, 1 model selected > select #1/A:1 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:1-264 4235 atoms, 4269 bonds, 264 residues, 1 model selected > color sel purple > color sel orange > 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> color sel #ff749aff > color sel #ff7499ff > color sel #ff7597ff > color sel #ff7791ff > color sel #ff778eff > color sel #ff778cff > color sel #ff778bff > color sel #ff778aff > color sel #ff788aff > color sel #ff7376ff > color sel #ff766eff > color sel #ff766cff > color sel #ff6f6aff > color sel #ff6267ff > color sel #ff546bff > color sel #ff4b6dff > color sel #ff476eff > color sel #ff486eff > color sel #ff5466ff > color sel #ff9050ff > color sel #ffa441ff > color sel #ffa93dff > color sel #ffa93cff > color sel #ffa734ff > color sel #ffa325ff > color sel #ff9f1bff > color sel #ffa01cff > color sel #ffa621ff > color sel #ffab27ff > color sel #ffad2aff > color sel #ffad2bff > color sel #ffac2bff > color sel #ffa92cff > color sel #ffa52cff > color sel #ff9d2cff > color sel #ff972cff > color sel #ff8d2dff > color sel #ff862eff > color sel #ff802fff > color sel #ff7a30ff > color sel #ff7631ff > color sel #ff7530ff > color sel #ff7430ff > color sel #ff7330ff > color sel #ff7130ff > color sel #ff6c30ff > color sel #ff6930ff > color sel #ff6830ff > color sel #ff672fff > color sel #ff642fff > color sel #ff602eff > color sel #ff5a2cff > color sel #ff562bff > color sel #ff512aff > color sel #ff4f2aff > color sel #ff4e2aff > color sel #ff4f2bff > color sel #ff5932ff > color sel #ff7140ff > color sel #ffaa63ff > color sel #ffd97bff > color sel #ffeb82ff > color sel #fdff85ff > color sel #f6ff85ff > color sel #eeff84ff > color sel #edff84ff > color sel #ecff84ff > color sel #eaff85ff > color sel #e2ff88ff > color sel #d9ff8aff > color sel #d5ff91ff > color sel #d1ff98ff > color sel #d0ff9bff > color sel #d2ff9eff > color sel #d3ffa1ff > color sel #d5ffa6ff > color sel #d7ffb5ff > color sel #d9ffc7ff > color sel #dbffd0ff > color sel #ddffd4ff > color sel #deffd7ff > color sel #deffd9ff > color sel #dfffdcff > color sel #ebfff0ff > color sel #effbffff > color sel #ecf5ffff > color sel #edf6ffff > color sel #eef9ffff > color sel #f1fbffff > color sel #f3fcffff > color sel #f7fdffff > color sel #fcfdffff > color sel #fff7f9ff > color sel #ffecedff > color sel #ffe7e9ff > color sel #ffe7e8ff > color sel #ffe6e8ff > color sel #ffe1e2ff > color sel #ffccd2ff > color sel #ffbdc9ff > color sel #ffbbc8ff > color sel #ffbaceff > color sel #ffb6d6ff > color sel #ffb7e2ff > color sel #ffbbf6ff > color sel #f7b6ffff > color sel #e9aaffff > color sel #d594ffff > color sel #cd89ffff > color sel #cc87ffff > color sel #cb87ffff > color sel #c981ffff > color sel #c172ffff > color sel #bc69ffff > color sel #bb66ffff > color sel #bb65ffff > color sel #bc66ffff > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select #1/A:1 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:1-433 7001 atoms, 7064 bonds, 433 residues, 1 model selected > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select #1/A:391 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:391-396 90 atoms, 91 bonds, 6 residues, 1 model selected > select #1/A:392 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:392-393 24 atoms, 24 bonds, 2 residues, 1 model selected > select #1/A:391 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:391-396 90 atoms, 91 bonds, 6 residues, 1 model selected > color sel yellow > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select #1/A:65 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/A:65-72 159 atoms, 160 bonds, 8 residues, 1 model selected > color sel yellow > select > #1/A:34-39,52-55,62-65,69-77,85-95,110-121,138-151,168-176,186-194,211-214,220-229,245-254,281-283,285-294,307-319,333-344,355-357,378-387,390-392,404-416,429-431 2930 atoms, 2937 bonds, 172 residues, 1 model selected > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select #1/A:391-392 28 atoms, 28 bonds, 2 residues, 1 model selected > select #1/A:391-397 100 atoms, 101 bonds, 7 residues, 1 model selected > color sel yellow > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > sequence chain #1/B Alignment identifier is 1/B > select #1/B:54 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/B:54-61 147 atoms, 149 bonds, 8 residues, 1 model selected > sequence chain #1/A Alignment identifier is 1/A > select #1/A:433 15 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:1-433 7001 atoms, 7064 bonds, 433 residues, 1 model selected > select #1/A:433 15 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:1-433 7001 atoms, 7064 bonds, 433 residues, 1 model selected > select #1/A:433 15 atoms, 14 bonds, 1 residue, 1 model selected > select #1/A:1-433 7001 atoms, 7064 bonds, 433 residues, 1 model selected > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select #1/B:61 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/B:54-61 147 atoms, 149 bonds, 8 residues, 1 model selected > select #1/B:37-44,58-64,89-92,98-108,124-130,162-170,178-185,218-223 1078 atoms, 1086 bonds, 60 residues, 1 model selected > select #1/B:54 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/B:54-61 147 atoms, 149 bonds, 8 residues, 1 model selected > select #1/B:54 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/B:54-61 147 atoms, 149 bonds, 8 residues, 1 model selected > select #1/B:54-55 43 atoms, 43 bonds, 2 residues, 1 model selected > select #1/B:54-61 147 atoms, 149 bonds, 8 residues, 1 model selected > select #1/B:54 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/B:54-61 147 atoms, 149 bonds, 8 residues, 1 model selected > select #1/B:54-55 43 atoms, 43 bonds, 2 residues, 1 model selected > select #1/B:54-62 157 atoms, 159 bonds, 9 residues, 1 model selected > color sel yellow > select #1/B:196-197 40 atoms, 40 bonds, 2 residues, 1 model selected > select #1/B:196-201 117 atoms, 117 bonds, 6 residues, 1 model selected > select add #1 10790 atoms, 10902 bonds, 660 residues, 1 model selected > select subtract #1 Nothing selected > select #1/B:1 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/B:1-18 301 atoms, 302 bonds, 18 residues, 1 model selected ===== 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 INTEL-18.5.8 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel 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: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14243.0.0,0) OS Loader Version: 540.100.7~23 Software: System Software Overview: System Version: macOS 12.3.1 (21E258) Kernel Version: Darwin 21.4.0 Time since boot: 4 days 1:21 Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina 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 }}} " defect closed normal Graphics nonchimerax all ChimeraX