id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18310 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x0000000549e83000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000548e77000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000547e6b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000546e5f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000545e53000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000544e47000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000543e3b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000542e2f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000541e23000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000540e17000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000053fe0b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000053edff000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000053ddf3000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000053cde7000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000051c807000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000052cc0f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000052bc03000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000052abf7000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000529beb000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000528bdf000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000527bd3000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000526bc7000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000525bbb000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000524baf000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000523ba3000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000522b97000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000521b8b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000520b7f000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000051fb73000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000051d92b000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File 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Please file a QTBUG which explains how to reproduce. > show #2 models > hide #!4 models > hide #4.1 models > view > show #2:ARG > show #2:LYS > show #2:GLU > show #2:ASP > select #2:SER 495 atoms, 456 bonds, 45 residues, 1 model selected > show sel atoms > style sel sphere Changed 495 atom styles > graphics silhouettes true > graphics silhouettes false > lighting soft > lighting full > lighting soft > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead > Lab/Postdoc/MD/SLC7A4_TM_Arginine/pr200ns_run1_whole_nojump_center_rotxyz- > transxyz.pdb"" Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive- Nexus365/Dimitris - Newstead Lab/Postdoc/MD/SLC7A4_TM_Arginine/pr200ns_run1_whole_nojump_center_rotxyz- transxyz.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX pr200ns_run1_whole_nojump_center_rotxyz-transxyz.pdb title: SLC7A4-Leu in POPC-Cholesterol in water t= 200000.00000 step= 100000000 [more info...] Chain information for pr200ns_run1_whole_nojump_center_rotxyz-transxyz.pdb #9 --- Chain | Description A | No description available Non-standard residues in pr200ns_run1_whole_nojump_center_rotxyz-transxyz.pdb #9 --- ACE — (ACE) CHL1 — (CHL1) CL — (CL) NA — (NA) NME — (NME) POPC — (popc) SOL — (SOL) ZR — (ZR) > hide #2 models > view > select #9:ZR 27 atoms, 26 bonds, 1 residue, 1 model selected > hide #9 atoms > select #9:ZR 27 atoms, 26 bonds, 1 residue, 1 model selected > show sel atoms > select sel : show sel atoms > view sel > ~display HC > select #9:ZR 27 atoms, 26 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel color #fffb00 interModel false distSlop 0.75 angleSlop 22.0 > twoColors true slopColor #ff9300 select true reveal true 17 hydrogen bonds found 9 strict hydrogen bonds found > hide sel cartoons > label sel > label height 0.5 > label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}"" > select clear > select add #9@@serial_number=29722 2 atoms, 2 residues, 1 model selected > select add #9/B:594@C 3 atoms, 3 residues, 1 model selected > select add #9@@serial_number=63161 4 atoms, 4 residues, 1 model selected > select add #9@@serial_number=34282 6 atoms, 6 residues, 1 model selected > select add #9@@serial_number=29141 8 atoms, 8 residues, 1 model selected > select add #9@@serial_number=90556 9 atoms, 9 residues, 1 model selected > select add #9@@serial_number=52898 11 atoms, 11 residues, 1 model selected > select add #9@@serial_number=40903 13 atoms, 13 residues, 1 model selected > select add #9@@serial_number=42401 15 atoms, 15 residues, 1 model selected > select add #9@@serial_number=94830 16 atoms, 16 residues, 1 model selected > select add #9@@serial_number=57339 18 atoms, 18 residues, 1 model selected > select add #9@@serial_number=90554 19 atoms, 18 residues, 1 model selected > select up 864 atoms, 846 bonds, 18 residues, 1 model selected > ui tool show H-Bonds > hbonds sel color #fffb00 interModel false distSlop 0.75 angleSlop 22.0 > twoColors true slopColor #ff9300 select true reveal true 92 hydrogen bonds found 58 strict hydrogen bonds found > select clear > hide #9 cartoons > select clear > hide #9.2 models > show #9.2 models > hide #9.1 models > show #9.1 models > camera mono > camera ortho > graphics silhouettes true > hide #9.1 models > hide #9.2 models > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead > Lab/Postdoc/MD/SLC7A4_TM_Arginine/pr200ns_run1_whole_nojump_center_rotxyz- > transxyz.xtc"" Replaced existing frames of pr200ns_run1_whole_nojump_center_rotxyz- transxyz.pdb #9 with 4001 new frames > show #9.1 models > hide #9.1 models > show #9.1 models > hide #9.1 models > color #9:ZR magenta > color #9:ZR byhetero swapaa cannot align to residues pr200ns_run1_whole_nojump_center_rotxyz- transxyz.pdb #9/? SOL 1207 which has fewer than 3 backbone atoms (N, C, CA) swapaa cannot align to residues pr200ns_run1_whole_nojump_center_rotxyz- transxyz.pdb #9/? SOL 2279 which has fewer than 3 backbone atoms (N, C, CA) > swapaa mousemode #9/A:336 SER > close #9 > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/MD/AtCAT4_leucine/pr1000ns/pr1000ns.gro"" Chain information for AtCAT4-Leu in POPC-Cholesterol in water #9 --- Chain | Description ? | No description available > hide #9:POPC,CHL1 > hide #9 atoms > select #9:ZL 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > view sel > select sel : show sel & #9 atoms > hide #9 models > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead > Lab/Postdoc/MD/AtCAT4_leucine/pr1000ns/pr1000ns_whole_nojump_center_rotxyz- > transxyz_skip10.xtc"" Replaced existing frames of AtCAT4-Leu in POPC-Cholesterol in water #9 with 2001 new frames > select add #4 4565 atoms, 4571 bonds, 670 residues, 3 models selected > select subtract #4 357 atoms, 243 bonds, 114 residues, 1 model selected > select add #9 158053 atoms, 124008 bonds, 35006 residues, 1 model selected > view > show #9 models > show sel cartoons > view > hide :9:SOL > hide :9:SOL,CL,NA > select clear > select #9/?:581@CA 1 atom, 1 residue, 1 model selected > select up 22 atoms, 21 bonds, 1 residue, 1 model selected > select sel : show sel atoms > ~display HC > view sel > close #9 > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead > Lab/Postdoc/MD/SLC7A4_homology_model_arginine_att2/pr1000ns/pr1000ns_whole_nojump_center_rotxyz- > transxyz.pdb"" Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive- Nexus365/Dimitris - Newstead Lab/Postdoc/MD/SLC7A4_homology_model_arginine_att2/pr1000ns/pr1000ns_whole_nojump_center_rotxyz- transxyz.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX pr1000ns_whole_nojump_center_rotxyz-transxyz.pdb title: SLC7A4-Leu in POPC-Cholesterol in water t= 1000000.00000 step= 500000000 [more info...] Chain information for pr1000ns_whole_nojump_center_rotxyz-transxyz.pdb #9 --- Chain | Description A | No description available Non-standard residues in pr1000ns_whole_nojump_center_rotxyz-transxyz.pdb #9 --- ACE — (ACE) CHL1 — (CHL1) CL — (CL) NA — (NA) NME — (NME) POPC — (popc) SOL — (SOL) ZR — (ZR) > select #9:ZR 27 atoms, 26 bonds, 1 residue, 1 model selected > view sel > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead > Lab/Postdoc/MD/SLC7A4_homology_model_arginine_att2/setup/step6.8_equilibration.gro"" Chain information for SLC7A4-Leu in POPC-Cholesterol in water #10 --- Chain | Description ? | No description available > hide #9 models > select #10/?:252 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead > Lab/Postdoc/MD/SLC7A4_homology_model_arginine_att2/setup/system_solvated_ions.gro"" Chain information for SLC7A4-Leu in POPC-Cholesterol in water #11 --- Chain | Description ? | No description available > matchmaker #11 to #10 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker SLC7A4-Leu in POPC-Cholesterol in water, chain (blank) (#10) with SLC7A4-Leu in POPC-Cholesterol in water, chain (blank) (#11), sequence alignment score = 2615.7 RMSD between 370 pruned atom pairs is 1.140 angstroms; (across all 555 pairs: 7.002) > hide #10 models > hide #11 models > show #9 models > close #9-11 > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/MD/AtCAT4_arginine/pr200ns_reps/run1/pr200ns_run1.gro"" Chain information for AtCAT4-Arg in POPC-Cholesterol in water #9 --- Chain | Description ? | No description available > select :ZR 27 atoms, 26 bonds, 1 residue, 1 model selected > view sel > select #9/?:243 12 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #9/?:327 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/MD/AtCAT4_arginine/pr200ns_reps/run2/pr200ns_run2.gro"" Chain information for AtCAT4-Arg in POPC-Cholesterol in water #10 --- Chain | Description ? | No description available > matchmaker #10 to #9 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#9) with AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#10), sequence alignment score = 2715.2 RMSD between 410 pruned atom pairs is 1.022 angstroms; (across all 551 pairs: 2.140) > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead > Lab/Postdoc/MD/AtCAT4_arginine/pr200ns_reps/run3/pr200ns_run3_whole_nojump_center_rotxyz- > transxyz.pdb"" Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive- Nexus365/Dimitris - Newstead Lab/Postdoc/MD/AtCAT4_arginine/pr200ns_reps/run3/pr200ns_run3_whole_nojump_center_rotxyz- transxyz.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX pr200ns_run3_whole_nojump_center_rotxyz-transxyz.pdb title: AtCAT4-Arg in POPC-Cholesterol in water t= 200000.00000 step= 100000000 [more info...] Chain information for pr200ns_run3_whole_nojump_center_rotxyz-transxyz.pdb #11 --- Chain | Description A | No description available Non-standard residues in pr200ns_run3_whole_nojump_center_rotxyz-transxyz.pdb #11 --- ACE — (ACE) CHL1 — (CHL1) CL — (CL) NA — (NA) NME — (NME) POPC — (popc) SOL — (SOL) ZR — (ZR) > matchmaker #11 to #9 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#9) with pr200ns_run3_whole_nojump_center_rotxyz-transxyz.pdb, chain A (#11), sequence alignment score = 2690 RMSD between 426 pruned atom pairs is 1.022 angstroms; (across all 551 pairs: 2.015) > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead > Lab/Postdoc/MD/AtCAT4_arginine/equilibration/step6.8_equilibration.gro"" Chain information for AtCAT4-Arg in POPC-Cholesterol in water #12 --- Chain | Description ? | No description available > matchmaker #12 to #9 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#9) with AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#12), sequence alignment score = 2549 RMSD between 378 pruned atom pairs is 1.139 angstroms; (across all 551 pairs: 5.844) > close #12 > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead Lab/Postdoc/MD/AtCAT4_arginine/charmm- > gui-0619450548/gromacs/step6.0_minimization.gro"" Chain information for AtCAT4-Arg in POPC-Cholesterol in water #12 --- Chain | Description ? | No description available > matchmaker #12 to #9 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#9) with AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#12), sequence alignment score = 2526.8 RMSD between 337 pruned atom pairs is 1.109 angstroms; (across all 551 pairs: 5.776) > hide #9 models > hide #10 models > hide #11 models > open ""/Users/ctn700/Library/CloudStorage/OneDrive- > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Ornithine/250630 - > newmodel_TM1 induced > fit/RealSpaceRefine_72/ORN_real_space_refined_063_mapJ510-coot-sn.pdb"" Chain information for ORN_real_space_refined_063_mapJ510-coot-sn.pdb #13 --- Chain | Description A | No description available B | No description available > matchmaker #13 to #12 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#12) with ORN_real_space_refined_063_mapJ510-coot-sn.pdb, chain A (#13), sequence alignment score = 2428.2 RMSD between 439 pruned atom pairs is 0.864 angstroms; (across all 506 pairs: 1.659) > dssp #13 > hide #12 models > show #12 models > select #12/?:47 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > select #13/A:47 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > dssp #12 > hide #12 models > show #9 models > select #9/?:47 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > show #10 models > hide #9 models > select #10/?:47 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > hide #10 models > show #11 models > select #11/A:48 19 atoms, 18 bonds, 1 residue, 1 model selected > select #11/A:48 19 atoms, 18 bonds, 1 residue, 1 model selected > select clear > select #11/A:47 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > show #13:HOH > select #13/A:117 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > close #2,4-6,9-12#1,3,7-8,13 > open ""/Users/ctn700/Library/CloudStorage/OneDrive- > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Figure > 1/revised_250722/1e/Fig1e_CAT4-ORN_updated_unsharpenedmap.cxs"" Opened cryosparc_P60_J427_008_volume_map_sharp.mrc as #6, grid size 288,288,288, pixel 0.835, shown at level 0.21, step 1, values float32 Opened cryosparc_P60_J510_006_volume_map_sharp.mrc as #9, grid size 576,576,576, pixel 0.417, shown at level 0.03, step 1, values float32 Opened cryosparc_P60_J510_005_volume_map.mrc as #10, grid size 576,576,576, pixel 0.417, shown at level 0.008, step 1, values float32 opened ChimeraX session > close #1,3-4#2,5-6 > hide #!9 models > show #!9 models > hide #!9 models > hide #!10 models > hide #!8 models > show #!8 models > show #!7 models > show #7 cartoons > hide #8 atoms > delete labels Missing or invalid ""atoms"" argument: invalid atoms specifier > delete label Missing or invalid ""atoms"" argument: invalid atoms specifier > delete #8 labels Expected a keyword > close #8.3#8.2 > show #8:CLR > show #8:CLR,LBN > view > ~display HC > color #8:CLR,LBN cronflowerblue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #8:CLR,LBN cornflowerblue > color #8:CLR,LBN byhetero > hide #8 cartoons > show #!9 models > select #8:CLR,LBN 416 atoms, 420 bonds, 4 residues, 1 model selected > select add #9 416 atoms, 420 bonds, 4 residues, 3 models selected > volume zone #9 nearAtoms sel & #8 range 2.5 > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2.5 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 4 > volume #9 level 0.02 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2 > select sel : show sel atoms > ~display HC > show sel cartoons > view > select #7/B:97 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 104 atoms, 105 bonds, 7 residues, 1 model selected > select up 1725 atoms, 1748 bonds, 114 residues, 1 model selected > select up 10144 atoms, 10262 bonds, 640 residues, 1 model selected > select down 1725 atoms, 1748 bonds, 114 residues, 1 model selected > color sel salmon cartoons > color sel salmon atoms > color sel atoms byhet Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel byhetero > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!8 models > hide #7 atoms > volume #10 level 0.01096 > hide #!10 models > show #!8 models > color #8/B salmon > color #8/B byhetero > hide #!7 models > show #!7 models > select clear > surface dust #9 size 4.17 > hide #!9 models > show #!9 models > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 3 > surface dust #9 size 4.17 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 3 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 1.5 > volume #9 level 0.015 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 1.6 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 1.8 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 1.9 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2.5 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 3 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 4 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2 > camera ortho > volume #9 level 0.019 > volume #9 level 0.02 > select #8:LBN 268 atoms, 266 bonds, 2 residues, 1 model selected > hide #!9 models > select #8:703 134 atoms, 133 bonds, 1 residue, 1 model selected > view sel > show #!9 models > select clear > ui tool show ""Side View"" > label #8 protein Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > select clear > volume #9 level 0.025 > volume #9 level 0.0106 > volume #9 level 0.01 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 1.5 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 3 > volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2 > volume #9 level 0.0208 > volume #9 level 0.025 > volume #9 level 0.03 > volume #9 level 0.025 > select #8:LBN,CLR 416 atoms, 420 bonds, 4 residues, 1 model selected > select sel : label sel > label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}"" > select #8:LBN,CLR 416 atoms, 420 bonds, 4 residues, 1 model selected > delete sel label Expected a keyword > delete label sel Missing or invalid ""atoms"" argument: invalid atoms specifier > ~label sel residues > select clear > graphics silhouettes false > graphics silhouettes true > select #8/C:703@O3 1 atom, 1 residue, 1 model selected > select up 134 atoms, 133 bonds, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel color #fffb00 interModel false distSlop 0.75 angleSlop 22.0 > twoColors true slopColor #ff9300 select true reveal true 0 hydrogen bonds found 0 strict hydrogen bonds found > hide #8.3 models > show #8.3 models > save LBN703.tiff supersample 8 transparentBackground true > save ""/Users/ctn700/Library/CloudStorage/OneDrive- > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids > figure/LBN703.cxs"" includeMaps true > save LBN703.tiff supersample 8 transparentBackground true > select #8:704 134 atoms, 133 bonds, 1 residue, 1 model selected > view sel > volume #9 level 0.02 > select clear > save LBN704.tiff supersample 8 transparentBackground true > save ""/Users/ctn700/Library/CloudStorage/OneDrive- > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids > figure/LBN704.cxs"" includeMaps true > select #8:702 74 atoms, 77 bonds, 1 residue, 1 model selected > view sel > select clear > volume #9 level 0.015 > volume #9 level 0.01 > volume #9 level 0.02 > show #!10 models > hide #!9 models > select add #10 2 models selected > surface dust #10 size 4.17 > show #!9 models > hide #!10 models > show #!10 models > hide #!9 models > select #8:701,702,703,704 499 atoms, 503 bonds, 4 residues, 1 model selected > volume zone #10 nearAtoms #8:CLR,LBN & #8 range 2 > volume #10 level 0.01 > volume #10 level 0.011 > volume zone #10 nearAtoms #8:CLR,LBN & #8 range 2.5 > volume zone #10 nearAtoms #8:CLR,LBN & #8 range 3 > volume zone #10 nearAtoms #8:CLR,LBN & #8 range 2 > select clear > save CLR702.tiff supersample 8 transparentBackground true > save ""/Users/ctn700/Library/CloudStorage/OneDrive- > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids > figure/CLR702.cxs"" includeMaps true > select #8:703 134 atoms, 133 bonds, 1 residue, 1 model selected > view sel > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > select clear > view > select #8:703 134 atoms, 133 bonds, 1 residue, 1 model selected > view sel > select clear > save ""/Users/ctn700/Library/CloudStorage/OneDrive- > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids > figure/LBN703.cxs"" includeMaps true > save LBN703.tiff supersample 8 transparentBackground true > select #8:704 134 atoms, 133 bonds, 1 residue, 1 model selected > view sel > select clear > save LBN704.tiff supersample 8 transparentBackground true > save ""/Users/ctn700/Library/CloudStorage/OneDrive- > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids > figure/LBN704.cxs"" includeMaps true > select #8:701 157 atoms, 160 bonds, 1 residue, 1 model selected > view sel No displayed objects specified. > view sel No displayed objects specified. > view sel No displayed objects specified. > view sel No displayed objects specified. > view sel No displayed objects specified. > select #8:701 157 atoms, 160 bonds, 1 residue, 1 model selected > view sel No displayed objects specified. > select #8:702 74 atoms, 77 bonds, 1 residue, 1 model selected > view sel > hide #!9 models > hide #!10 models > show #!9 models > show #!10 models > select #8:705 74 atoms, 77 bonds, 1 residue, 1 model selected > view sel > select #8:701 157 atoms, 160 bonds, 1 residue, 1 model selected > view sel No displayed objects specified. > view sel No displayed objects specified. > view sel No displayed objects specified. > view sel No displayed objects specified. > select #8:705 74 atoms, 77 bonds, 1 residue, 1 model selected > view sel > select clear > save CLR705.tiff supersample 8 transparentBackground true > save ""/Users/ctn700/Library/CloudStorage/OneDrive- > Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids > figure/CLR705.cxs"" includeMaps true > rainbow > color #7 tan > undo > transparency #7 0 cartoons > color byhetero > select #8:704 134 atoms, 133 bonds, 1 residue, 1 model selected > view sel > select #8:703 134 atoms, 133 bonds, 1 residue, 1 model selected > select #8:702 74 atoms, 77 bonds, 1 residue, 1 model selected > view sel > select #8:704 134 atoms, 133 bonds, 1 residue, 1 model selected > view sel > view > select #8:704 134 atoms, 133 bonds, 1 residue, 1 model selected > view sel > select #8:703 134 atoms, 133 bonds, 1 residue, 1 model selected > view sel > select clear > color bychain > select #8:705 74 atoms, 77 bonds, 1 residue, 1 model selected > view sel > select clear > rainbow > color byhetero > select #7/B:62 12 atoms, 11 bonds, 1 residue, 1 model selected > select up 39 atoms, 38 bonds, 3 residues, 1 model selected > select up 1725 atoms, 1748 bonds, 114 residues, 1 model selected > color sel bychain > select up 10144 atoms, 10262 bonds, 640 residues, 1 model selected > select down 1725 atoms, 1748 bonds, 114 residues, 1 model selected > select clear > open ""/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris - > Newstead > Lab/Postdoc/MD/AtCAT4_ornithine_EM_model/production_from_IFD/pr1000ns_run1_whole_nojump_center_rotxyz- > transxyz.pdb"" Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive- Nexus365/Dimitris - Newstead Lab/Postdoc/MD/AtCAT4_ornithine_EM_model/production_from_IFD/pr1000ns_run1_whole_nojump_center_rotxyz- transxyz.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb title: AtCAT4-Orn cryoEM structure in POPC-Cholesterol in water t= 137500.00000 step= 68750000 [more info...] Chain information for pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb #1 --- Chain | Description A | No description available Non-standard residues in pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb #1 --- ACE — (ACE) CHL1 — (CHL1) CL — (CL) NA — (NA) NME — (NME) ORN — (ORN) POPC — (popc) SOL — (SOL) > matchmaker #7 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb, chain A (#8) with ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb, chain A (#7), sequence alignment score = 2699.8 RMSD between 518 pruned atom pairs is 0.000 angstroms; (across all 518 pairs: 0.000) > hide #!8 models > show #!8 models > hide #!7 models > show #!7 models > matchmaker #1 to #8 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb, chain A (#8) with pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb, chain A (#1), sequence alignment score = 2453.2 RMSD between 392 pruned atom pairs is 1.068 angstroms; (across all 518 pairs: 2.352) > hide #!7 models > hide #!8 models > hide #8.2 models > hide #8.3 models > hide #1 atoms > protein | #1:CHL1,POPC /A | #1:CHL1,POPC select /A | #1:CHL1,POPC select #1:CHL1,POPC & (/A: show sel atoms > select #1:CHL1,POPC & (/A: hide sel atoms > select #1:CHL1,POPC & (/A: hide sel cartoons > hide sel atoms > select #1:CHL1,POPC & (/A: show sel atoms > color sel bychain > color sel byhetero > color :CHL1 yellow > color :CHL1 byhetero > color :POPC red > color :POPC byhetero > ~display HC > select clear > view > show #!8 models > show #!7 models > view > hide #!8 models > show #!8 models > hide #!7 models > hide #!8 models > view > show #!7 models > hide #!7 models > select #1/A:27 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > show #!8 models > hide #!8 models > show #!7 models > select #1/C:586@C4 1 atom, 1 residue, 1 model selected > select up 74 atoms, 77 bonds, 1 residue, 1 model selected > view sel > hide #1 models > dssp > hide #!9 models > hide #!10 models > hide #!7 models > show #!7 models > close #8.2 > close #8.3 > close #7.2 > show #!8 models > hide #8 atoms > select #8/A:250,251,253,257,340,333,178,32 158 atoms, 151 bonds, 8 residues, 1 model selected > show sel atoms > show #8/A:250,251,253,257,340,333,178,32 cartoons > transparency #7 75 cartoons > hide #8 cartoons > show #8/A:250,251,253,257,340,333,178,32 cartoons > ~display HC > select #8/A:250,251,253,257,340,333,178,32 158 atoms, 151 bonds, 8 residues, 1 model selected > view sel > combine #8 > show #2:ARG,LYS,HIS,GLU,ASP > ~display HC > hide #!2 models > show #!2 models > hide #!7 models > show #!7 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > hide sel atoms > select up 24 atoms, 23 bonds, 1 residue, 1 model selected > hide sel atoms > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select add #8/A:251@OE2 1 atom, 1 bond, 1 residue, 1 model selected > select add #8/A:340@HH22 2 atoms, 2 bonds, 2 residues, 1 model selected > select add #8/A:32@OD1 3 atoms, 2 bonds, 3 residues, 1 model selected > select add #8/A:178@NZ 4 atoms, 2 bonds, 4 residues, 1 model selected > select up 8 atoms, 2 bonds, 6 residues, 1 model selected > select up 112 atoms, 107 bonds, 6 residues, 1 model selected > ui tool show H-Bonds > hbonds sel color #fffb00 interModel false distSlop 0.75 angleSlop 22.0 > twoColors true slopColor #ff9300 select true 18 hydrogen bonds found 9 strict hydrogen bonds found > show sel atoms > undo > ui tool show H-Bonds > select #8/A:250,251,253,257,340,333,178,32 158 atoms, 151 bonds, 6 pseudobonds, 8 residues, 2 models selected > ui tool show H-Bonds > hbonds sel color #fffb00 interModel false relax false distSlop 0.75 > angleSlop 22.0 twoColors true slopColor #ff9300 saltOnly true select true 3 hydrogen bonds found 3 strict hydrogen bonds found > ui tool show H-Bonds > hbonds sel color #fffb00 showDist true interModel false relax false distSlop > 0.75 angleSlop 22.0 twoColors true slopColor #ff9300 saltOnly true select > true 3 hydrogen bonds found 3 strict hydrogen bonds found > color #8.2.1 black models > addh #8:178 Summary of feedback from adding hydrogens to copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8 --- notes | No usable SEQRES records for copy of ORN_real_space_refined_063_mapJ510-coot-isolde2_real_space_refined_072-coot.pdb (#8) chain A; guessing termini instead No usable SEQRES records for copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb (#8) chain B; guessing termini instead Chain-initial residues that are actual N termini: copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/A PRO 21, copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/B GLN 1 Chain-initial residues that are not actual N termini: copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/A TYR 456 Chain-final residues that are actual C termini: copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/B SER 114 Chain-final residues that are not actual C termini: copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/A ALA 583, copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/A GLY 410 515 hydrogen bonds copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/A ALA 583 is not terminus, removing H atom from 'C' 0 hydrogens added > ui mousemode right minimize Missing atoms or parameterization needed by force field. All heavy atoms and hydrogens with standard names are required. Error with ignoreExternalBonds=False was No template found for residue 390 (GLY). The set of atoms matches GLY, but the bonds are different. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template Error with ignoreExternalBonds=True was Multiple non-identical matching templates found for residue 80 (CYS): CYM, CYX. > distance #8/A:32@OD2 #8/A:178@HZ1 Distance between copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/A ASP 32 OD2 and LYS 178 HZ1: 2.7Å > hide #8.2.1 models > show #8.2.1 models > hide #!8.2 models > show #!8.2 models > distance #8/A:32@OD2 #8/A:178@HZ3 Distance between copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/A ASP 32 OD2 and LYS 178 HZ3: 2.3Å > distance #8/A:32@OD2 #8/A:178@HZ2 Distance between copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/A ASP 32 OD2 and LYS 178 HZ2: 3.3Å > hide #3.1 models > show #3.1 models > hide #!3 models > show #!3 models > close #3 > distance #8/A:32@OD2 #8/A:178@HZ3 Distance between copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb #8/A ASP 32 OD2 and LYS 178 HZ3: 2.3Å > color #3 #fffc79ff models > hide #3.1 models > show #3.1 models > color #3.1 black models > select clear > color #3 #fffb00ff models > color #3 black models > color #8.2 #fff800ff models > color #3 #fff800ff models > color #3.1 #008f00ff models > color #3.1 black models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 22 atoms, 21 bonds, 1 residue, 1 model selected > hide sel atoms > hide sel cartoons > select clear > select #8/A:250,251,257,340,333,178,32 136 atoms, 130 bonds, 4 pseudobonds, 7 residues, 3 models selected > select #8/A:250,251,340,333,178,32 112 atoms, 107 bonds, 4 pseudobonds, 6 residues, 3 models selected > select #7/A:257 24 atoms, 23 bonds, 1 residue, 1 model selected > hide sel cartoons > select #8/A:257 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > hide sel cartoons > show #!2 models > hide #!2 models > hide #7.1 models > show #7.1 models > hide #!7 models > show #!7 models > show #7 cartoons > select #8/A:250,251,340,333,178,32 112 atoms, 107 bonds, 4 pseudobonds, 6 residues, 3 models selected > label sel > label height 0.5 > label height 0.75 > label (#!8 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > select clear > color #7 cartoon white Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #7 white cartoons > color #7 tan cartoons > color #8.3 #4f8f00ff models > color #8.3 #009193ff models > color #8.3 black models > color #8.2.1 black models > show #!10 models > hide #!10 models > select #8/A:250,251,340,333,178,32 112 atoms, 107 bonds, 4 pseudobonds, 6 residues, 3 models selected > show #!10 models > volume zone #10 nearAtoms sel & #8 range 2.5 > volume zone #10 nearAtoms sel & #8 range 2 > show #!9 models Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic models, 2 maps. > hide #!10 models > volume zone #9 nearAtoms sel & #8 range 2.5 > volume zone #10 nearAtoms sel & #8 range 2 > show #!10 models > volume #10 level 0.013 > hide #!9 models > show #!9 models > hide #!10 models > volume #9 level 0.03 > volume zone #10 nearAtoms sel & #8 range 1.9 > volume zone #9 nearAtoms sel & #8 range 1.9 > volume zone #9 nearAtoms sel & #8 range 2 > hide #!9 models > color #7 grey cartoons > color #7 lightgrey cartoons > color #7 white cartoons > color #7 lightgrey cartoons > color #7 gainsboro cartoons > color #7 lightgrey cartoons > select clear > select add #7 10144 atoms, 10262 bonds, 1 pseudobond, 640 residues, 2 models selected > hide #!7 models > show #!7 models > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb_A SES surface #7.2: minimum, -13.38, mean 0.08, maximum 16.25 Coulombic values for ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb_B SES surface #7.3: minimum, -11.94, mean 1.05, maximum 9.69 To also show corresponding color key, enter the above coulombic command and add key true > hide #!7.2 models > show #7.2 models > hide #!7.3 models > show #7.3 models > hide #!7.3 models > hide #!7.2 models > show #7.3 models > hide #!7.3 models > show #7.3 models > hide #!7.3 models > show #7.3 models > hide #!7.3 models > show #7.2 models > color #7.2 #00000033 > show #7.3 models > color #7.2 black > close #7.2-3 > toolshed show > coulombic sel Coulombic values for ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb_A SES surface #7.2: minimum, -13.38, mean 0.08, maximum 16.25 Coulombic values for ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb_B SES surface #7.3: minimum, -11.94, mean 1.05, maximum 9.69 To also show corresponding color key, enter the above coulombic command and add key true > close #7.2-3 > select #8/A:250,251,340,333,178,32 112 atoms, 107 bonds, 4 pseudobonds, 6 residues, 3 models selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for copy of ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb_A SES surface #8.4: minimum, -15.51, mean 0.01, maximum 16.24 > close #8.4 > select clear > select add #7 10144 atoms, 10262 bonds, 1 pseudobond, 640 residues, 2 models selected > coulombic sel Coulombic values for ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb_A SES surface #7.2: minimum, -13.38, mean 0.08, maximum 16.25 Coulombic values for ORN_real_space_refined_063_mapJ510-coot- isolde2_real_space_refined_072-coot.pdb_B SES surface #7.3: minimum, -11.94, mean 1.05, maximum 9.69 To also show corresponding color key, enter the above coulombic command and add key true > color #7.3 transparent > color #7.3 black > color #7.2 transparent > color #7.2 #00000041 > color #7.2 transparent > color #7.2 #0000003e > color #7.2 #0000003d > close #7.2-3 > select clear > color #7 grey cartoons > select clear > save electrostaticgate.tiff supersample 8 transparentBackground true > show #!9 models > show #!10 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!10 models > show #!10 models > hide #!10 models > show #!9 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > hide #8.2.1 models > hide #8.3 models > hide #3.1 models > hide #!3 models > hide #!8.2 models > hide #!8 models > show #!8 models > hide #7.1 models > show #7.1 models Cell requested for row 4 is out of bounds for table with 13 rows! Resizing table model. > hide #!7 models > hide #!8 models > save electrostaticgate_density.tiff supersample 8 transparentBackground true > show #!7 models > show #!8 models > transparency #7 0 cartoons > show #!8.2 models > show #8.2.1 models > show #8.3 models > hide #!9 models > show #3.1 models > hide #!3 models > show #!3 models > select #8:orn 22 atoms, 21 bonds, 1 residue, 1 model selected > style sel sphere Changed 22 atom styles > show sel atoms ===== Log before crash end ===== Log: Startup Messages --- warning | Registration file '/Users/ctn700/Library/Application Support/ChimeraX/registration' has expired note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,6 Model Number: MNWA3DK/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 6 days, 15 hours, 51 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 38 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2720Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 30.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.24.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.9 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-LigandRecognizer: 0.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-locscalesurfer: 0.1.1 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-PICKLUSTER: 2.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-TugLigands: 1.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 einops: 0.3.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 fsspec: 2025.5.1 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 mpmath: 1.3.0 mrcfile: 1.3.0 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.24.4 numpy: 1.26.4 openvr: 1.26.701 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.10.1 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 sympy: 1.14.0 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 timm: 0.4.12 tinyarray: 1.2.4 tomli: 2.0.1 torch: 2.2.2 torchvision: 0.17.2 tornado: 6.4.2 tqdm: 4.66.6 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX